Modules

Revision as of 10:50, 9 April 2019 (view source) Louistw@uab.edu (Talk | contribs) ← Older edit		Latest revision as of 12:02, 13 June 2019 (view source) Louistw@uab.edu (Talk | contribs)
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	This list is not exhaustive and may not reflect the accurate current versions of the different software installed on the system. Please see the output of the ''module avail'' command for the official list of software modules installed on Cheaha.		This list is not exhaustive and may not reflect the accurate current versions of the different software installed on the system. Please see the output of the ''module avail'' command for the official list of software modules installed on Cheaha.
−	Last Update: 2019-04-09	+	Last Update: 2019-06-13
	__NOTOC__		__NOTOC__
	<p class="toc">'''Contents:'''  | [[#A|A]] | [[#B|B]] | [[#C|C]] | [[#D|D]] | [[#E|E]] | [[#F|F]] | [[#G|G]] | [[#H|H]] | [[#I|I]] | [[#J|J]] | [[#K|K]] | [[#L|L]] | [[#M|M]] | [[#N|N]] | [[#O|O]] | [[#P|P]] | [[#Q|Q]] | [[#R|R]] | [[#S|S]] | [[#T|T]] | [[#U|U]] | [[#V|V]] | [[#W|W]] | [[#X|X]] | [[#Y|Y]] | [[#Z|Z]]</p>		<p class="toc">'''Contents:'''  | [[#A|A]] | [[#B|B]] | [[#C|C]] | [[#D|D]] | [[#E|E]] | [[#F|F]] | [[#G|G]] | [[#H|H]] | [[#I|I]] | [[#J|J]] | [[#K|K]] | [[#L|L]] | [[#M|M]] | [[#N|N]] | [[#O|O]] | [[#P|P]] | [[#Q|Q]] | [[#R|R]] | [[#S|S]] | [[#T|T]] | [[#U|U]] | [[#V|V]] | [[#W|W]] | [[#X|X]] | [[#Y|Y]] | [[#Z|Z]]</p>
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	|[[#Bismark|'''Bismark''']]		|[[#Bismark|'''Bismark''']]
	|0.19.0-foss-2016a		|0.19.0-foss-2016a
−	|- style="vertical-align:top;"
−
−	|[[#Bison|'''Bison''']]
−	|3.0.4-GCCcore-7.3.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 344:		Line 340:
	|[[#dvctools|'''dvctools''']]		|[[#dvctools|'''dvctools''']]
−	|1.0	+	|recommended
	|}		|}
	==E==		==E==
Line 471:		Line 467:
	|[[#flex|'''flex''']]		|[[#flex|'''flex''']]
	|2.6.3-GCCcore-7.3.0		|2.6.3-GCCcore-7.3.0
−	|- style="vertical-align:top;"
−
−	|[[#fontconfig|'''fontconfig''']]
−	|2.12.1-GCCcore-5.4.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 483:		Line 475:
	|[[#freeglut|'''freeglut''']]		|[[#freeglut|'''freeglut''']]
	|3.0.0-intel-2017a		|3.0.0-intel-2017a
−	|- style="vertical-align:top;"
−
−	|[[#freetype|'''freetype''']]
−	|2.6.5-GCCcore-5.4.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 566:		Line 554:
	|[[#GDAL|'''GDAL''']]		|[[#GDAL|'''GDAL''']]
	|2.2.3-foss-2018a-Python-3.6.4		|2.2.3-foss-2018a-Python-3.6.4
−	|- style="vertical-align:top;"
−
−	|[[#GMP|'''GMP''']]
−	|6.1.2-GCCcore-5.4.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
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	|[[#GObject-Introspection|'''GObject-Introspection''']]		|[[#GObject-Introspection|'''GObject-Introspection''']]
	|1.48.0-foss-2016a		|1.48.0-foss-2016a
−	|- style="vertical-align:top;"
−
−	|[[#GSL|'''GSL''']]
−	|1.16-foss-2016b
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 590:		Line 570:
	|[[#Gdk-Pixbuf|'''Gdk-Pixbuf''']]		|[[#Gdk-Pixbuf|'''Gdk-Pixbuf''']]
	|2.36.10-intel-2017a		|2.36.10-intel-2017a
−	|- style="vertical-align:top;"
−
−	|[[#Ghostscript|'''Ghostscript''']]
−	|9.19-intel-2016a
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 602:		Line 578:
	|[[#gcccuda|'''gcccuda''']]		|[[#gcccuda|'''gcccuda''']]
	|2018b		|2018b
−	|- style="vertical-align:top;"
−
−	|[[#gettext|'''gettext''']]
−	|0.19.8-GCCcore-5.4.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
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	|[[#goolf|'''goolf''']]		|[[#goolf|'''goolf''']]
	|1.7.20		|1.7.20
−	|- style="vertical-align:top;"
−
−	|[[#gperf|'''gperf''']]
−	|3.0.4-foss-2016b
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
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	|[[#IPython|'''IPython''']]		|[[#IPython|'''IPython''']]
	|5.0.0-foss-2016a-Python-3.5.1		|5.0.0-foss-2016a-Python-3.5.1
−	|- style="vertical-align:top;"
−
−	|[[#ImageMagick|'''ImageMagick''']]
−	|7.0.2-5-intel-2016a
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
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	|[[#intel|'''intel''']]		|[[#intel|'''intel''']]
	|mic/sdk/3.8.4		|mic/sdk/3.8.4
−	|- style="vertical-align:top;"
−
−	|[[#intltool|'''intltool''']]
−	|0.51.0-GCCcore-5.4.0-Perl-5.24.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 847:		Line 807:
	|[[#JUnit|'''JUnit''']]		|[[#JUnit|'''JUnit''']]
	|4.12-Java-1.8.0_92		|4.12-Java-1.8.0_92
−	|- style="vertical-align:top;"
−
−	|[[#JasPer|'''JasPer''']]
−	|2.0.14-GCCcore-6.4.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
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	|[[#LAPACK|'''LAPACK''']]		|[[#LAPACK|'''LAPACK''']]
	|3.4.2-gompi-1.5.12		|3.4.2-gompi-1.5.12
−	|- style="vertical-align:top;"
−
−	|[[#LLVM|'''LLVM''']]
−	|3.7.1-foss-2016b
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
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	|[[#LibTIFF|'''LibTIFF''']]		|[[#LibTIFF|'''LibTIFF''']]
	|4.0.9-GCCcore-5.4.0		|4.0.9-GCCcore-5.4.0
−	|- style="vertical-align:top;"
−
−	|[[#LittleCMS|'''LittleCMS''']]
−	|2.7-intel-2016a
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 1,041:		Line 989:
	|[[#libdrm|'''libdrm''']]		|[[#libdrm|'''libdrm''']]
	|2.4.91-GCCcore-5.4.0		|2.4.91-GCCcore-5.4.0
−	|- style="vertical-align:top;"
−
−	|[[#libffi|'''libffi''']]
−	|3.2.1-GCCcore-5.4.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 1,081:		Line 1,025:
	|[[#libpciaccess|'''libpciaccess''']]		|[[#libpciaccess|'''libpciaccess''']]
	|0.13.4-intel-2016a		|0.13.4-intel-2016a
−	|- style="vertical-align:top;"
−
−	|[[#libpng|'''libpng''']]
−	|1.6.24-GCCcore-5.4.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
	|[[#libpthread-stubs|'''libpthread-stubs''']]		|[[#libpthread-stubs|'''libpthread-stubs''']]
	|0.3-intel-2016a		|0.3-intel-2016a
−	|- style="vertical-align:top;"
−
−	|[[#libreadline|'''libreadline''']]
−	|7.0-GCCcore-5.4.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
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	|[[#matlab|'''matlab''']]		|[[#matlab|'''matlab''']]
−	|R2017b	+	|R2019a
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
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	|[[#MVAPICH2|'''MVAPICH2''']]		|[[#MVAPICH2|'''MVAPICH2''']]
	|2.2b-GCC-4.9.3-2.25		|2.2b-GCC-4.9.3-2.25
−	|- style="vertical-align:top;"
−
−	|[[#Mako|'''Mako''']]
−	|1.0.7-foss-2016b-Python-2.7.14
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 1,347:		Line 1,279:
	|[[#ncdu|'''ncdu''']]		|[[#ncdu|'''ncdu''']]
	|1.13-20.1		|1.13-20.1
		+	|- style="vertical-align:top;"
		+
		+	|[[#nighres|'''nighres''']]
		+	|1.1.0b1
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
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	|[[#ncbi-vdb|'''ncbi-vdb''']]		|[[#ncbi-vdb|'''ncbi-vdb''']]
	|2.7.0-foss-2016b		|2.7.0-foss-2016b
−	|- style="vertical-align:top;"
−
−	|[[#netCDF-Fortran|'''netCDF-Fortran''']]
−	|4.4.4-intel-2016a
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
	|[[#netCDF|'''netCDF''']]		|[[#netCDF|'''netCDF''']]
	|4.6.0-foss-2018a		|4.6.0-foss-2018a
−	|- style="vertical-align:top;"
−
−	|[[#nettle|'''nettle''']]
−	|3.4-foss-2016b
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 1,541:		Line 1,469:
	|[[#perl-app-cpanminus|'''perl-app-cpanminus''']]		|[[#perl-app-cpanminus|'''perl-app-cpanminus''']]
	|1.7039		|1.7039
−	|- style="vertical-align:top;"
−
−	|[[#picard|'''picard''']]
−	|2.10.0-Java-1.8.0_74
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
	|[[#pixman|'''pixman''']]		|[[#pixman|'''pixman''']]
	|0.34.0-GCCcore-5.4.0		|0.34.0-GCCcore-5.4.0
−	|- style="vertical-align:top;"
−
−	|[[#pkg-config|'''pkg-config''']]
−	|0.29.2-foss-2016b
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 1,702:		Line 1,622:
	!Latest version		!Latest version
		+	|- style="vertical-align:top;"
		+
		+	|[[#snakemakeslurm_local|'''snakemakeslurm_local''']]
		+	|4.8.0-1
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 1,726:		Line 1,650:
	|[[#S.A.G.E.|'''S.A.G.E.''']]		|[[#S.A.G.E.|'''S.A.G.E.''']]
	|6.3		|6.3
−	|- style="vertical-align:top;"
−
−	|[[#SAMtools|'''SAMtools''']]
−	|1.4.1-intel-2017a
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 1,754:		Line 1,674:
	|[[#SPPARKS|'''SPPARKS''']]		|[[#SPPARKS|'''SPPARKS''']]
	|07192016-intel-2016a		|07192016-intel-2016a
−	|- style="vertical-align:top;"
−
−	|[[#SQLite|'''SQLite''']]
−	|3.21.0-GCCcore-5.4.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 1,770:		Line 1,686:
	|[[#SWIG|'''SWIG''']]		|[[#SWIG|'''SWIG''']]
	|3.0.12-foss-2018a-Python-2.7.14		|3.0.12-foss-2018a-Python-2.7.14
−	|- style="vertical-align:top;"
−
−	|[[#Salmon|'''Salmon''']]
−	|0.9.1-foss-2016b-Python-2.7.12
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 1,857:		Line 1,769:
	|[[#Tar|'''Tar''']]		|[[#Tar|'''Tar''']]
	|1.29-goolf-1.4.10		|1.29-goolf-1.4.10
−	|- style="vertical-align:top;"
−
−	|[[#Tcl|'''Tcl''']]
−	|8.6.8-GCCcore-5.4.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 1,885:		Line 1,793:
	|[[#tabix|'''tabix''']]		|[[#tabix|'''tabix''']]
	|0.2.6-intel-2015b		|0.2.6-intel-2015b
−	|- style="vertical-align:top;"
−
−	|[[#tbb|'''tbb''']]
−	|2017_U5-foss-2016b
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 1,924:		Line 1,828:
	!Latest version		!Latest version
−	|- style="vertical-align:top;"
−
−	|[[#util-linux|'''util-linux''']]
−	|2.31.1-GCCcore-5.4.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 1,997:		Line 1,897:
	|[[#xget|'''xget''']]		|[[#xget|'''xget''']]
	|xget-public		|xget-public
−	|- style="vertical-align:top;"
−
−	|[[#X11|'''X11''']]
−	|20180131-GCCcore-5.4.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
	|[[#XKeyboardConfig|'''XKeyboardConfig''']]		|[[#XKeyboardConfig|'''XKeyboardConfig''']]
	|2.17-intel-2016a		|2.17-intel-2016a
−	|- style="vertical-align:top;"
−
−	|[[#XML-Parser|'''XML-Parser''']]
−	|2.44_01-GCCcore-5.4.0-Perl-5.24.0
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
Line 2,099:		Line 1,991:
	!Latest version		!Latest version
−	|- style="vertical-align:top;"
−
−	|[[#ZeroMQ|'''ZeroMQ''']]
−	|4.1.4-foss-2016a
	|- style="vertical-align:top;"		|- style="vertical-align:top;"
	|[[#zlib|'''zlib''']]		|[[#zlib|'''zlib''']]
	|1.2.9-intel-2017a		|1.2.9-intel-2017a
		+	|- style="vertical-align:top;"
		+
		+	|[[#ZeroMQ|'''ZeroMQ''']]
		+	|4.1.4-foss-2016a
	|}		|}
	==Software Detail==		==Software Detail==
Line 2,307:		Line 2,199:
	Command: ''module load Bismark''		Command: ''module load Bismark''
−
−	===Bison===
−
−	Homepage: http://www.gnu.org/software/bison
−
−	Description: Bison is a general-purpose parser generator that converts an annotated context-free grammarinto a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
−
−	Available versions: 2.7-foss-2016a, 3.0.2-intel-2015b, 3.0.4, 3.0.4-GCC-4.9.3-2.25, 3.0.4-GCC-4.9.3-binutils-2.25, 3.0.4-GCCcore-4.9.3, 3.0.4-GCCcore-5.4.0, 3.0.4-GCCcore-6.3.0, 3.0.4-foss-2016a, 3.0.4-foss-2016b, 3.0.4-goolf-1.7.20, 3.0.4-intel-2015b, 3.0.4-intel-2016a, 3.0.4-GCCcore-6.1.0, 2.7-GCCcore-6.3.0, 2.7, 3.0.4-GCCcore-6.4.0, 3.0.4-intel-2017a, 3.0.4-GCCcore-7.3.0
−
−	Command: ''module load Bison''
	===Bowtie===		===Bowtie===
Line 2,670:		Line 2,552:
	===dvctools===		===dvctools===
−	Available versions: 0.3, recommended, 0.4, 0.5, 0.6, 0.7, 0.8, latest, 0.9, 0.2, 1.0	+	Available versions: 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.2, 1.0, latest, recommended
	Command: ''module load dvctools''		Command: ''module load dvctools''
Line 2,887:		Line 2,769:
	Command: ''module load flex''		Command: ''module load flex''
−
−	===fontconfig===
−
−	Homepage: http://www.freedesktop.org/software/fontconfig
−
−	Description: Fontconfig is a library designed to provide system-wide font configuration, customization andapplication access.
−
−	Available versions: 2.11.1-intel-2015b, 2.11.1-intel-2016a, 2.11.94-foss-2016a, 2.11.94-foss-2016b, 2.11.95-intel-2016a, 2.12.1-foss-2016b, 2.12.1-intel-2015b, 2.12.1-intel-2016a, 2.12.1-GCCcore-6.3.0-libpng-1.6.29, 2.12.4-GCCcore-6.4.0, 2.12.1-intel-2017a, 2.11.94-intel-2016a, 2.11.95-foss-2016b, 2.11.95-foss-2016a, 2.12.6-GCCcore-6.4.0, 2.12.1-GCCcore-5.4.0-libpng-1.6.29, 2.12.6-GCCcore-5.4.0, 2.12.1-GCCcore-5.4.0
−
−	Command: ''module load fontconfig''
	===fontsproto===		===fontsproto===
Line 2,913:		Line 2,785:
	Command: ''module load freeglut''		Command: ''module load freeglut''
−
−	===freetype===
−
−	Homepage: http://freetype.org
−
−	Description: FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, andportable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, displayservers, font conversion tools, text image generation tools, and many other products as well.
−
−	Available versions: 2.5.3-intel-2015b, 2.6-intel-2015b, 2.6.2-foss-2016a, 2.6.2-foss-2016b, 2.6.2-goolf-1.7.20, 2.6.2-intel-2016a, 2.6.3-foss-2016a, 2.6.3-intel-2016a, 2.6.5-foss-2016b, 2.6.5-intel-2015b, 2.6.5-intel-2016a, 2.7-foss-2016b, 2.7.1-GCCcore-6.3.0-libpng-1.6.29, 2.7.1-goolf-1.7.20-libpng-1.6.18, 2.8-GCCcore-6.4.0, 2.6.5-intel-2017a, 2.6.3-foss-2016b, 2.6.5-intel-2016b, 2.6-intel-2016a, 2.6-intel-2016b, 2.6.2-intel-2016b, 2.9-GCCcore-6.4.0, 2.7.1-GCCcore-5.4.0-libpng-1.6.29, 2.9-GCCcore-5.4.0, 2.6.5-GCCcore-5.4.0
−
−	Command: ''module load freetype''
	===FastQ_Screen===		===FastQ_Screen===
Line 3,067:		Line 2,929:
	Command: ''module load GDAL''		Command: ''module load GDAL''
−
−	===GMP===
−
−	Homepage: http://gmplib.org/
−
−	Description: GMP is a free library for arbitrary precision arithmetic,operating on signed integers, rational numbers, and floating point numbers.
−
−	Available versions: 5.0.5-goolf-1.4.10, 5.0.5-goolf-1.7.20, 6.0.0a-GCC-4.8.4, 6.0.0a-GNU-4.9.3-2.25, 6.1.0-foss-2016a, 6.1.0-foss-2016b, 6.1.0-goolf-1.7.20, 6.1.0-intel-2015b, 6.1.0-intel-2016a, 6.1.1-foss-2016a, 6.1.1-foss-2016b, 6.1.1-intel-2015b, 6.1.1-intel-2016a, 6.1.2-GCCcore-6.3.0, 6.1.1-intel-2017a, 6.1.2-GCCcore-6.4.0, 4.3.2, 6.1.2-GCCcore-5.4.0
−
−	Command: ''module load GMP''
	===GNU===		===GNU===
Line 3,093:		Line 2,945:
	Command: ''module load GObject-Introspection''		Command: ''module load GObject-Introspection''
−
−	===GSL===
−
−	Homepage: http://www.gnu.org/software/gsl/
−
−	Description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.The library provides a wide range of mathematical routines such as random number generators, special functionsand least-squares fitting.
−
−	Available versions: 1.16-goolf-1.7.20, 1.16-intel-2015b, 2.1-foss-2015b, 2.1-foss-2016a, 2.1-intel-2016a, 2.3-foss-2016b, 1.16-foss-2016b
−
−	Command: ''module load GSL''
	===GTK+===		===GTK+===
Line 3,123:		Line 2,965:
	Command: ''module load Gdk-Pixbuf''		Command: ''module load Gdk-Pixbuf''
−
−	===Ghostscript===
−
−	Available versions: 9.19-intel-2016a
−
−	Command: ''module load Ghostscript''
	===gawk===		===gawk===
Line 3,145:		Line 2,981:
	Command: ''module load gcccuda''		Command: ''module load gcccuda''
−
−	===gettext===
−
−	Homepage: http://www.gnu.org/software/gettext/
−
−	Description: GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we maybuild many other steps. This package offers to programmers, translators, and even users, a well integrated set of toolsand documentation
−
−	Available versions: 0.19.2-goolf-1.7.20, 0.19.2-intel-2015b, 0.19.6-GNU-4.9.3-2.25, 0.19.6-foss-2016a, 0.19.6-foss-2016b, 0.19.6-intel-2015b, 0.19.6-intel-2016a, 0.19.7-intel-2016a, 0.19.8, 0.19.8-foss-2016a, 0.19.8-foss-2016b, 0.19.8-intel-2015b, 0.19.8-intel-2016a, 0.19.8.1, 0.19.8.1-GCCcore-6.3.0, 0.19.6, 0.19.8.1-GCCcore-6.4.0, 0.19.8-intel-2017a, 0.19.4-intel-2015b, 0.19.7-foss-2016b, 0.19.7-foss-2016a, 0.19.8.1-GCCcore-6.4.0-libxml2-2.9.7, 0.19.8.1-GCCcore-5.4.0, 0.19.8.1-GCCcore-5.4.0-libxml2-2.9.7, 0.19.8-GCCcore-5.4.0
−
−	Command: ''module load gettext''
	===glproto===		===glproto===
Line 3,183:		Line 3,009:
	Command: ''module load goolf''		Command: ''module load goolf''
−
−	===gperf===
−
−	Homepage: http://www.gnu.org/software/gperf/
−
−	Description: GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hashfunction and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hashfunction is perfect, which means that the hash table has no collisions, and the hash table lookup needs a singlestring comparison only.
−
−	Available versions: 3.0.4-goolf-1.7.20, 3.0.4-intel-2016a, 3.1-GCCcore-6.4.0, 3.1-GCCcore-5.4.0, 3.0.4-foss-2016b
−
−	Command: ''module load gperf''
	===grep===		===grep===
Line 3,425:		Line 3,241:
	Command: ''module load IPython''		Command: ''module load IPython''
−
−	===ImageMagick===
−
−	Available versions: 7.0.2-5-intel-2016a
−
−	Command: ''module load ImageMagick''
	===icc===		===icc===
Line 3,503:		Line 3,313:
	Command: ''module load intel''		Command: ''module load intel''
−
−	===intltool===
−
−	Homepage: http://freedesktop.org/wiki/Software/intltool/
−
−	Description: intltool is a set of tools to centralize translation ofmany different file formats using GNU gettext-compatible PO files.
−
−	Available versions: 0.51.0-intel-2016a-Perl-5.22.1, 0.51.0-intel-2017a-Perl-5.24.1, 0.51.0-GCCcore-6.4.0-Perl-5.26.0, 0.51.0-GCCcore-6.4.0-Perl-5.26.1, 0.51.0-GCCcore-5.4.0-Perl-5.26.1, 0.51.0-GCCcore-5.4.0-Perl-5.24.0
−
−	Command: ''module load intltool''
	===ITK===		===ITK===
Line 3,569:		Line 3,369:
	Command: ''module load JUnit''		Command: ''module load JUnit''
−
−	===JasPer===
−
−	Homepage: http://www.ece.uvic.ca/~frodo/jasper/
−
−	Description: The JasPer Project is an open-source initiative to provide a freesoftware-based reference implementation of the codec specified inthe JPEG-2000 Part-1 standard.
−
−	Available versions: 1.900.1-intel-2016a, 1.900.1-intel-2017a, 1.900.1-foss-2016b, 2.0.14-GCCcore-6.4.0
−
−	Command: ''module load JasPer''
	===Java===		===Java===
Line 3,675:		Line 3,465:
	Command: ''module load LAPACK''		Command: ''module load LAPACK''
−
−	===LLVM===
−
−	Homepage: http://llvm.org/
−
−	Description: The LLVM Core libraries provide a modern source- and target-independentoptimizer, along with code generation support for many popular CPUs(as well as some less common ones!) These libraries are built around a wellspecified code representation known as the LLVM intermediate representation("LLVM IR"). The LLVM Core libraries are well documented, and it isparticularly easy to invent your own language (or port an existing compiler)to use LLVM as an optimizer and code generator.
−
−	Available versions: 3.7.1-intel-2016a, 3.8.0-intel-2016a, 3.8.1-foss-2016b, 4.0.0-intel-2017a, 5.0.1-GCCcore-6.4.0, 5.0.1-GCCcore-5.4.0, 3.7.1-foss-2016b
−
−	Command: ''module load LLVM''
	===LeadIT===		===LeadIT===
Line 3,701:		Line 3,481:
	Command: ''module load LibTIFF''		Command: ''module load LibTIFF''
−
−	===LittleCMS===
−
−	Available versions: 2.7-intel-2016a
−
−	Command: ''module load LittleCMS''
	===Lmod===		===Lmod===
Line 3,885:		Line 3,659:
	Command: ''module load libdrm''		Command: ''module load libdrm''
−
−	===libffi===
−
−	Homepage: http://sourceware.org/libffi/
−
−	Description: The libffi library provides a portable, high level programming interface to various callingconventions. This allows a programmer to call any function specified by a call interface description at run-time.
−
−	Available versions: 3.1-goolf-1.7.20, 3.1-intel-2015b, 3.2.1-GNU-4.9.3-2.25, 3.2.1-foss-2016a, 3.2.1-foss-2016b, 3.2.1-intel-2015b, 3.2.1-intel-2016a, 3.2.1-GCCcore-6.3.0, 3.2.1-intel-2017a, 3.2.1-GCCcore-6.4.0, 3.2.1-intel-2016b, 3.2.1-GCCcore-5.4.0
−
−	Command: ''module load libffi''
	===libfontenc===		===libfontenc===
Line 3,965:		Line 3,729:
	Command: ''module load libpciaccess''		Command: ''module load libpciaccess''
−
−	===libpng===
−
−	Homepage: http://www.libpng.org/pub/png/libpng.html
−
−	Description: libpng is the official PNG reference library
−
−	Available versions: 1.5.13-goolf-1.7.20, 1.6.10-intel-2015b, 1.6.10-intel-2016a, 1.6.12-intel-2015b, 1.6.12-intel-2016a, 1.6.16-goolf-1.7.20, 1.6.16-intel-2015b, 1.6.17-foss-2015b, 1.6.17-goolf-1.7.20, 1.6.17-intel-2015b, 1.6.2-goolf-1.4.10, 1.6.2-goolf-1.7.20, 1.6.21-foss-2016a, 1.6.21-foss-2016b, 1.6.21-goolf-1.7.20, 1.6.21-intel-2015b, 1.6.21-intel-2016a, 1.6.23-foss-2016a, 1.6.23-foss-2016b, 1.6.23-intel-2015b, 1.6.23-intel-2016a, 1.6.24-foss-2016b, 1.6.24-intel-2015b, 1.6.24-intel-2016a, 1.6.26-foss-2016b, 1.6.29-intel-2016a, 1.6.29-GCCcore-6.3.0, 1.6.18-goolf-1.7.20, 1.6.32-GCCcore-6.4.0, 1.6.24-intel-2017a, 1.6.24-intel-2016b, 1.6.17-intel-2016a, 1.6.17-intel-2016b, 1.6.21-intel-2016b, 1.6.34-GCCcore-6.4.0, 1.6.29-GCCcore-5.4.0, 1.6.34-GCCcore-5.4.0, 1.6.24-GCCcore-5.4.0
−
−	Command: ''module load libpng''
	===libpthread-stubs===		===libpthread-stubs===
Line 3,981:		Line 3,735:
	Command: ''module load libpthread-stubs''		Command: ''module load libpthread-stubs''
−
−	===libreadline===
−
−	Homepage: http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html
−
−	Description: The GNU Readline library provides a set of functions for use by applications thatallow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available.The Readline library includes additional functions to maintain a list of previously-entered command lines,to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
−
−	Available versions: 6.2-foss-2016a, 6.2-goolf-1.4.10, 6.2-goolf-1.7.20, 6.3-GNU-4.9.3-2.25, 6.3-foss-2015b, 6.3-foss-2016a, 6.3-foss-2016b, 6.3-goolf-1.7.20, 6.3-intel-2015b, 6.3-intel-2016a, 7.0-GCCcore-6.3.0, 6.2-intel-2016a, 6.3-intel-2017a, 7.0-GCCcore-6.4.0, 7.0-GCCcore-5.4.0
−
−	Command: ''module load libreadline''
	===libsodium===		===libsodium===
Line 4,170:		Line 3,914:
	===matlab===		===matlab===
−	Available versions: R2012a, R2013a, R2015a, R2015b, R2016a, R2016b, R2017a, R2018a, R2017b	+	Available versions: R2012a, R2013a, R2015a, R2015b, R2016a, R2016b, R2017a, R2018a, R2017b, R2019a
	Command: ''module load rc/matlab''		Command: ''module load rc/matlab''
Line 4,263:		Line 4,007:
	Command: ''module load MVAPICH2''		Command: ''module load MVAPICH2''
−
−	===Mako===
−
−	Homepage: http://www.makotemplates.org
−
−	Description: A super-fast templating language that borrows the best ideas from the existing templating languages
−
−	Available versions: 1.0.4-foss-2016b-Python-2.7.12, 1.0.6-intel-2017a-Python-2.7.13, 1.0.7-foss-2018a-Python-2.7.14, 1.0.7-foss-2016b-Python-2.7.14
−
−	Command: ''module load Mako''
	===Maq===		===Maq===
Line 4,457:		Line 4,191:
	Command: ''module load rc/ncdu''		Command: ''module load rc/ncdu''
		+
		+	===nighres===
		+
		+	Available versions: 1.1.0b1
		+
		+	Command: ''module load rc/nighres''
	===NASM===		===NASM===
Line 4,479:		Line 4,219:
	Command: ''module load ncbi-vdb''		Command: ''module load ncbi-vdb''
−
−	===netCDF-Fortran===
−
−	Available versions: 4.4.4-intel-2016a
−
−	Command: ''module load netCDF-Fortran''
	===netCDF===		===netCDF===
Line 4,495:		Line 4,229:
	Command: ''module load netCDF''		Command: ''module load netCDF''
−
−	===nettle===
−
−	Homepage: http://www.lysator.liu.se/~nisse/nettle/
−
−	Description: Nettle is a cryptographic library that is designed to fit easilyin more or less any context: In crypto toolkits for object-orientedlanguages (C++, Python, Pike, ...), in applications like LSH or GNUPG,or even in kernel space.
−
−	Available versions: 3.1.1-GNU-4.9.3-2.25, 3.2-foss-2016b, 3.2-intel-2016a, 3.3-intel-2017a, 3.3-GCCcore-6.4.0, 3.2-intel-2017a, 3.4-foss-2018a, 3.3-foss-2016b, 3.4-foss-2016b
−
−	Command: ''module load nettle''
	===nodejs===		===nodejs===
Line 4,795:		Line 4,519:
	Command: ''module load perl-app-cpanminus''		Command: ''module load perl-app-cpanminus''
−
−	===picard===
−
−	Available versions: 2.1.1-Java-1.8.0_74, 2.10.0-Java-1.8.0_74
−
−	Command: ''module load picard''
	===pixman===		===pixman===
Line 4,811:		Line 4,529:
	Command: ''module load pixman''		Command: ''module load pixman''
−
−	===pkg-config===
−
−	Homepage: http://www.freedesktop.org/wiki/Software/pkg-config/
−
−	Description: pkg-config is a helper tool used when compiling applications and libraries. It helps you insert thecorrect compiler options on the command line so an application can usegcc -o test test.c `pkg-config --libs --cflags glib-2.0`for instance, rather than hard-coding values on where to find glib (or other libraries).
−
−	Available versions: 0.28-GNU-4.9.3-2.25, 0.29-foss-2016a, 0.29-foss-2016b, 0.29-goolf-1.7.20, 0.29-intel-2016a, 0.29.1-foss-2016b, 0.29.1-intel-2015b, 0.29.1-intel-2016a, 0.29.1-GCCcore-6.3.0, 0.29.1-intel-2017a, 0.29.2-GCCcore-6.4.0, 0.29.2-GCCcore-5.4.0, 0.29.1-GCCcore-5.4.0, 0.29.2-foss-2016b
−
−	Command: ''module load pkg-config''
	===pkgconfig===		===pkgconfig===
Line 5,073:		Line 4,781:
	Command: ''module load Rust''		Command: ''module load Rust''
		+
		+	===snakemakeslurm_local===
		+
		+	Available versions: 4.8.0-1
		+
		+	Command: ''module load snakemakeslurm_local''
	===SAS===		===SAS===
Line 5,109:		Line 4,823:
	Command: ''module load S.A.G.E.''		Command: ''module load S.A.G.E.''
−
−	===SAMtools===
−
−	Homepage: http://www.htslib.org/
−
−	Description: SAM Tools provide various utilities for manipulating alignments in the SAM format,including sorting, merging, indexing and generating alignments in a per-position format.
−
−	Available versions: 0.1.19-foss-2016a, 0.1.19-goolf-1.7.20, 1.3.1-foss-2016a, 1.3.1-intel-2015b, 1.5-intel-2017a, 1.6-intel-2017a, 1.6-intel-2016a, 1.3.1-intel-2017a-HTSlib-1.3.2, 1.4.1-intel-2017a
−
−	Command: ''module load SAMtools''
	===SCOTCH===		===SCOTCH===
Line 5,159:		Line 4,863:
	Command: ''module load SPPARKS''		Command: ''module load SPPARKS''
−
−	===SQLite===
−
−	Homepage: http://www.sqlite.org/
−
−	Description: SQLite: SQL Database Engine in a C Library
−
−	Available versions: 3.13.0-foss-2016a, 3.13.0-foss-2016b, 3.13.0-intel-2015b, 3.13.0-intel-2016a, 3.8.10.2-goolf-1.7.20, 3.8.10.2-intel-2015b, 3.8.8.1-foss-2015b, 3.8.8.1-goolf-1.7.20, 3.8.8.1-intel-2015b, 3.9.2-foss-2016a, 3.9.2-foss-2016b, 3.9.2-goolf-1.7.20, 3.9.2-intel-2015b, 3.9.2-intel-2016a, 3.17.0-GCCcore-6.3.0, 3.8.9-foss-2016a, 3.8.5-goolf-1.4.10, 3.8.5-intel-2016a, 3.13.0-intel-2017a, 3.20.1-GCCcore-6.4.0, 3.21.0-GCCcore-6.4.0, 3.17.0-GCCcore-5.4.0, 3.20.1-GCCcore-5.4.0, 3.21.0-GCCcore-5.4.0
−
−	Command: ''module load SQLite''
	===STAR-Fusion===		===STAR-Fusion===
Line 5,191:		Line 4,885:
	Command: ''module load SWIG''		Command: ''module load SWIG''
−
−	===Salmon===
−
−	Homepage: https://github.com/COMBINE-lab/salmon
−
−	Description: Salmon is a wicked-fast program to produce a highly-accurate,transcript-level quantification estimates from RNA-seq data.
−
−	Available versions: 0.5.1-intel-2015b-Python-2.7.10, 0.7.2-intel-2015b-Python-2.7.10, 0.8.2-foss-2016b-Python-2.7.12, 0.9.1-foss-2016b-Python-2.7.12
−
−	Command: ''module load Salmon''
	===ScientificPython===		===ScientificPython===
Line 5,331:		Line 5,015:
	Command: ''module load Tar''		Command: ''module load Tar''
−
−	===Tcl===
−
−	Homepage: http://www.tcl.tk/
−
−	Description: Tcl (Tool Command Language) is a very powerful but easy to learn dynamicprogramming language, suitable for a very wide range of uses, including weband desktop applications, networking, administration, testing and many more.
−
−	Available versions: 8.5.12-goolf-1.4.10, 8.5.16-intel-2016a, 8.6.3-foss-2015b, 8.6.3-goolf-1.7.20, 8.6.3-intel-2015b, 8.6.4-foss-2015b, 8.6.4-foss-2016a, 8.6.4-foss-2016b, 8.6.4-goolf-1.7.20, 8.6.4-intel-2015b, 8.6.4-intel-2016a, 8.6.5-foss-2016a, 8.6.5-foss-2016b, 8.6.5-intel-2015b, 8.6.5-intel-2016a, 8.6.6-GCCcore-6.3.0, 8.6.4-goolf-1.4.10, 8.6.5-intel-2017a, 8.6.8-GCCcore-6.4.0, 8.6.7-GCCcore-6.4.0, 8.6.6-GCCcore-5.4.0, 8.6.7-GCCcore-5.4.0, 8.6.8-GCCcore-5.4.0
−
−	Command: ''module load Tcl''
	===Tk===		===Tk===
Line 5,381:		Line 5,055:
	Command: ''module load tabix''		Command: ''module load tabix''
−
−	===tbb===
−
−	Homepage: https://01.org/tbb/
−
−	Description: Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs thattake full advantage of multicore performance, that are portable, composable and have future-proof scalability.
−
−	Available versions: 2017_U6-intel-2017a, 2017_U5-intel-2017a, 2017_U6-intel-2016a, 2017_U5-foss-2016b
−
−	Command: ''module load tbb''
	===tcsh===		===tcsh===
Line 5,445:		Line 5,109:
	Command: ''module load torque''		Command: ''module load torque''
−
−	===util-linux===
−
−	Homepage: http://www.kernel.org/pub/linux/utils/util-linux
−
−	Description: Set of Linux utilities
−
−	Available versions: 2.26.1-intel-2015b, 2.27.1-foss-2016a, 2.28-foss-2016a, 2.28-intel-2016a, 2.29.2-intel-2017a, 2.30.1-GCCcore-6.3.0, 2.31-GCCcore-6.4.0, 2.31.1-GCCcore-6.4.0, 2.31.1-GCCcore-5.4.0
−
−	Command: ''module load util-linux''
	===unblur===		===unblur===
Line 5,547:		Line 5,201:
	Command: ''module load rc/xget''		Command: ''module load rc/xget''
−
−	===X11===
−
−	Homepage: https://www.x.org
−
−	Description: The X Window System (X11) is a windowing system for bitmap displays
−
−	Available versions: 20160819-foss-2016b, 20160819-intel-2015b, 20160819-intel-2016a, 20170314-GCCcore-6.3.0, 20171023-GCCcore-6.4.0, 20180131-GCCcore-6.4.0, 20180131-GCCcore-5.4.0
−
−	Command: ''module load X11''
	===XKeyboardConfig===		===XKeyboardConfig===
Line 5,563:		Line 5,207:
	Command: ''module load XKeyboardConfig''		Command: ''module load XKeyboardConfig''
−
−	===XML-Parser===
−
−	Homepage: http://search.cpan.org/~toddr/XML-Parser-2.41/
−
−	Description: This is a Perl extension interface to James Clark's XML parser, expat.
−
−	Available versions: 2.44-intel-2016a-Perl-5.22.1, 2.44_01-intel-2017a-Perl-5.24.1, 2.44_01-GCCcore-6.4.0-Perl-5.26.0, 2.44_01-GCCcore-6.4.0-Perl-5.26.1, 2.44_01-GCCcore-5.4.0-Perl-5.26.1, 2.44_01-GCCcore-5.4.0-Perl-5.24.0
−
−	Command: ''module load XML-Parser''
	===xbitmaps===		===xbitmaps===
Line 5,717:		Line 5,351:
	Command: ''module load Yasm''		Command: ''module load Yasm''
−
−	===ZeroMQ===
−
−	Available versions: 3.2.5-intel-2015b, 4.1.4-foss-2016a
−
−	Command: ''module load ZeroMQ''
	===zlib===		===zlib===
Line 5,730:		Line 5,358:
	Description: zlib is designed to be a free, general-purpose, legally unencumbered -- that is,not covered by any patents -- lossless data-compression library for use on virtually anycomputer hardware and operating system.		Description: zlib is designed to be a free, general-purpose, legally unencumbered -- that is,not covered by any patents -- lossless data-compression library for use on virtually anycomputer hardware and operating system.
−	Available versions: 1.2.11-GCCcore-6.3.0, 1.2.11-intel-2016a, 1.2.5-goolf-1.4.10, 1.2.5-goolf-1.7.20, 1.2.7-foss-2016a, 1.2.7-goolf-1.4.10, 1.2.7-goolf-1.7.20, 1.2.7-intel-2015b, 1.2.7-intel-2016a, 1.2.8, 1.2.8-GCC-4.9.3-binutils-2.25, 1.2.8-GCCcore-4.9.3, 1.2.8-GCCcore-5.4.0, 1.2.8-GNU-4.9.3-2.25, 1.2.8-foss-2015b, 1.2.8-foss-2016a, 1.2.8-foss-2016b, 1.2.8-goolf-1.4.10, 1.2.8-goolf-1.7.20, 1.2.8-intel-2015b, 1.2.8-intel-2016a, 1.2.8-GCCcore-6.1.0, 1.2.8-intel-2017a, 1.2.11, 1.2.11-GCCcore-6.4.0, 1.2.8-intel-2016b, 1.2.11-GCCcore-7.3.0, 1.2.11-GCCcore-5.4.0, 1.2.9-intel-2017a	+	Available versions: 1.2.10, 1.2.11-GCCcore-6.3.0, 1.2.11-intel-2016a, 1.2.5-goolf-1.4.10, 1.2.5-goolf-1.7.20, 1.2.7-foss-2016a, 1.2.7-goolf-1.4.10, 1.2.7-goolf-1.7.20, 1.2.7-intel-2015b, 1.2.7-intel-2016a, 1.2.8, 1.2.8-GCC-4.9.3-binutils-2.25, 1.2.8-GCCcore-4.9.3, 1.2.8-GCCcore-5.4.0, 1.2.8-GNU-4.9.3-2.25, 1.2.8-foss-2015b, 1.2.8-foss-2016a, 1.2.8-foss-2016b, 1.2.8-goolf-1.4.10, 1.2.8-goolf-1.7.20, 1.2.8-intel-2015b, 1.2.8-intel-2016a, 1.2.8-GCCcore-6.1.0, 1.2.8-intel-2017a, 1.2.11, 1.2.11-GCCcore-6.4.0, 1.2.8-intel-2016b, 1.2.11-GCCcore-7.3.0, 1.2.11-GCCcore-5.4.0, 1.2.9-intel-2017a
	Command: ''module load zlib''		Command: ''module load zlib''
		+
		+	===ZeroMQ===
		+
		+	Available versions: 3.2.5-intel-2015b, 4.1.4-foss-2016a
		+
		+	Command: ''module load ZeroMQ''

---

Latest revision as of 12:02, 13 June 2019

This page shows a list of installed modules on the Cheaha research computing system. If you don't find a particular package listed on this page, please send a request to cheaha support to request the software.

This list is not exhaustive and may not reflect the accurate current versions of the different software installed on the system. Please see the output of the module avail command for the official list of software modules installed on Cheaha.

Last Update: 2019-06-13

Contents: | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z

[edit] A

Name	Latest version
anvio	3
atom	1.30.0
AFNI	18.2.05-intel-2016a-Python-2.7.11
ANTs	2.1.0rc3-foss-2016a
APBS	1.4-linux-static-x86_64
ASHS	2.0.0_07202018
ATK	2.26.0-intel-2017a
ATLAS	3.10.1-gompi-1.5.12-LAPACK-3.4.2
Amber	14-intel-2016a-AmberTools-15-patchlevel-13-13
Anaconda2	4.2.0
Aspera-Connect	3.6.1
AutoDock_Vina	1.1.2_linux_x86
Autoconf	2.69-GCCcore-5.4.0
annovar	2016Feb01-foss-2015b-Perl-5.22.1
ant	1.9.7-Java-1.8.0_92
ABySS	2.0.2-foss-2016a
Anaconda3	5.3.0
aaf-phylogeny	20160831
acml	gcc/mp/fma4/5.3.1

[edit] B

Name	Latest version
BrainSuite	15b
basespace-cli	0.8.12
brainstorm	180709
BEDTools	2.26.0-foss-2016a
BSMAP	2.90-foss-2016a
BWA	0.7.13-intel-2016a
BXH_XCEDE_TOOLS	1.11.1
BamTools	2.4.0-intel-2016a
Bismark	0.19.0-foss-2016a
Bowtie	1.1.2-foss-2016a
Bowtie2	2.3.3-intel-2017a
BreakDancer	1.4.5-intel-2016a
BCFtools	1.6-intel-2016a
BLAST+	2.6.0-intel-2017a-Python-2.7.13
Biopython	1.70-intel-2017a-Python-3.6.1
bioitx	jupyter
blacs	openmpi/gcc/64/1.1patch03
blas	gcc/64/3.8.0
bonnie++	1.97.3

[edit] C

Name	Latest version
cmg	2016.101.GU
cytoscape	2.8.2
cellranger	2.2.0
crossmap	0.2.8
chezscheme	9.5
ceres	1.13.0
CBLAS	20110120-foss-2016b
CD-HIT	4.6.8-intel-2017a
CHARMM	40b1-intel-2016a
CHASE	v1
CUDA	9.2.88-GCC-7.3.0-2.30
Circos	0.69-5-intel-2016a-Perl-5.18.2
ConnectomeWorkbench	1.3.1
Cufflinks	2.2.1-goolf-1.7.20
cairo	1.14.12-GCCcore-6.4.0
configurable-http-proxy	1.3.0-foss-2016a-nodejs-4.4.7
cutadapt	1.12
CTFFIND	4.1.8-foss-2016b
cuDNN	7.0.5-CUDA-9.0.176
ctffind	4.0.17-foss-2016b
cluster-tools-dell	8.1
cluster-tools	8.1
cuda90	toolkit/9.0.176
cuda91	toolkit/9.1.85
cuda80	toolkit/8.0.61
cuda10.0	toolkit/10.0.130
cuda92	toolkit/9.2.88

[edit] D

Name	Latest version
delly	0.7.6
dsistudio	dsistudio-20151020
detonate	1.11
dicombrowser	1.7.0b5
drracket	7.1
DBus	1.11.20-intel-2017a
DMTCP	2.5.0
Doxygen	1.8.13-GCCcore-6.4.0
damageproto	1.2.1-intel-2016a
dbus-glib	0.108-intel-2017a
DB	6.2.32-intel-2017a
dvctools	recommended

[edit] E

Name	Latest version
EMAN2	2.2
EIGENSOFT	6.1.4-foss-2016b
ENT	1.0.2
EPACTS	3.2.6-foss-2016b
Elk	4.3.6-intel-2016a
Emacs	24.5-GCC-4.9.3-2.25
entrypoints	0.2.2-foss-2016a-Python-3.5.1
eudev	3.1.5-foss-2016b
EDGE_pro	1.3.1
exonerate	2.2.0
EDGE_pro_patch	1.3.1-2

[edit] F

Name	Latest version
FSL	6.0.0
fdtd	8.17.1157-1
freesurfer	Dev/10_29_16
fpart	1.1.0
freeimage	3.18
FASTX-Toolkit	0.0.14-intel-2015b
FIAT	1.6.0-intel-2015b-Python-2.7.11
FLTK	1.3.3-foss-2016b
FLUENT	19.1
FSL	5.0.10-intel-2017a
FastQC	0.11.7-Java-1.8.0_74
FastTree	2.1.9-goolf-1.4.10
FreeSurfer	6.0.0-centos6_x86_64
fastPHASE	1.4.8
file	5.28-foss-2016b
fixesproto	5.0-foss-2016a
flex	2.6.3-GCCcore-7.3.0
fontsproto	2.1.3-intel-2016a
freeglut	3.0.0-intel-2017a
FastQ_Screen	0.11.2
Firefox	44.0.2
FreeXL	1.0.2-intel-2016a
freebayes	1.1.0-goolf-1.7.20_39e5e4b
frealign	9.11-intel-2016a-avx-mp
FriBidi	1.0.1-foss-2016b
freeipmi	1.5.7
fftw2	openmpi/gcc/64/float/2.1.5
fftw3	openmpi/gcc/64/3.3.7

[edit] G

Name	Latest version
GEMMA	GEMMA_Rec
gromacs-intel	2018.1
GeneTorrent	GeneTorrent_4.0.0-9
GATK	3.7-Java-1.8.0_92
GC3Pie	2.4.2
GCC	7.3.0-2.30
GCCcore	7.3.0
GD	2.52-intel-2016a-Perl-5.18.2
GDAL	2.2.3-foss-2018a-Python-3.6.4
GNU	4.9.3-2.25
GObject-Introspection	1.48.0-foss-2016a
GTK+	2.24.31-intel-2017a
Gdk-Pixbuf	2.36.10-intel-2017a
gawk	4.0.2-goolf-1.4.10
gcccuda	2018b
glproto	1.4.17-foss-2016b
gnuplot	5.0.3-intel-2016a
gnutls	3.4.7-GNU-4.9.3-2.25
goolf	1.7.20
grep	2.15-goolf-1.4.10
groff	1.22.2-foss-2016b
gtool	0.7.5_linux_x86_64
guile	1.8.8-GNU-4.9.3-2.25
GEOS	3.6.2-foss-2018a-Python-3.6.4
GStreamer	1.8.3-foss-2016a
GConf	3.2.6-intel-2017a
GST-plugins-base	0.10.36-intel-2017a
gdc-client	1.3.0-intel-2016a-Python-2.7.12
Gctf	1.06_devel
gzip	1.6
gcc	7.2.0
gdb	8.0.1
globalarrays	openmpi/gcc/64/5.6.1

[edit] H

Name	Latest version
hydrasv	0.5.3
HOMER	4.9
HAPGEN2	2.2.0
HISAT2	2.1.0-foss-2016b
HPL	2.2-intel-2016a
HTSeq	0.6.1p1-intel-2015b-Python-2.7.8
HarfBuzz	1.5.1-intel-2017a
Hypre	2.10.1-intel-2015b
h5py	2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16
help2man	1.47.4-GCCcore-5.4.0
hwloc	1.11.8
HMMER	3.1b2-intel-2016a
hdf5	1.10.1
hdf5_18	1.8.20
hpl	2.2

[edit] I

Name	Latest version
intel	compiler/64/ps_2016/2016.0.047
IMPUTE2	2.3.2_x86_64_static
IPython	5.0.0-foss-2016a-Python-3.5.1
icc	2016.3.210-GCC-5.4.0-2.26
iccifort	2016.3.210-GCC-5.4.0-2.26
ifort	2016.3.210-GCC-5.4.0-2.26
iimpi	2016b
imkl	11.3.3.210-iimpi-2016b
impi	5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26
inputproto	2.3.1-intel-2016a
intel	mic/sdk/3.8.4
ITK	4.12.2-foss-2016b-Python-2.7.12
ICU	61.1-GCCcore-6.4.0
ipmitool	1.8.18
intel-tbb-oss	intel64/2018_20180618oss
iozone	3_471

[edit] J

Name	Latest version
jspr	2017-7-20
JAGS	3.4.0-goolf-1.4.10
JUnit	4.12-Java-1.8.0_92
Java	.modulerc
Jellyfish	2.2.6-foss-2016b
jupyterhub	0.6.1-foss-2016a-Python-3.5.1

[edit] K

Name	Latest version
Kent_tools	340
Kerberos_V5	1.12.2-intel-2015b
kbproto	1.0.7-intel-2016a
KING	2.1.2-foss-2016a
kallisto	0.43.1-intel-2017a

[edit] L

Name	Latest version
lstc	lsdyna
lumpy	0.2.13
lcmodel	6.3
luajit	2.0.5
libarchive	3.1.2-10
LAPACK	3.4.2-gompi-1.5.12
LeadIT	2.1.9
LibTIFF	4.0.9-GCCcore-5.4.0
Lmod	6.3-GCC-4.8.4
LocusZoom	1.3-goolf-1.7.20
Lua	5.1.4-8-GCC-4.8.4
lftp	4.6.4-GNU-4.9.3-2.25
libGLU	9.0.0-foss-2018a
libICE	1.0.9-intel-2016a
libSM	1.2.2-intel-2016a
libX11	1.6.3-intel-2016a
libXau	1.0.8-intel-2016a
libXcursor	1.1.14-foss-2016b
libXdamage	1.1.4-intel-2016a
libXdmcp	1.1.2-intel-2016a
libXext	1.3.3-intel-2016a
libXfixes	5.0.1-intel-2016a
libXfont	1.5.1-intel-2016a-freetype-2.6.3
libXft	2.3.2-foss-2016b
libXi	1.7.6-intel-2016a
libXinerama	1.1.3-foss-2016b
libXmu	1.1.2-intel-2016a
libXp	1.0.3-intel-2016a
libXpm	3.5.11-intel-2016a
libXrandr	1.5.0-intel-2016a
libXrender	0.9.9-intel-2016a
libXt	1.1.5-intel-2016a
libcerf	1.4-intel-2016a
libdrm	2.4.91-GCCcore-5.4.0
libfontenc	1.1.3-intel-2016a
libgcrypt	1.6.5-intel-2017a
libgd	2.2.4-intel-2017a
libglade	2.6.4-intel-2016a
libgpg-error	1.21-intel-2017a
libgtextutils	0.6.1-intel-2015b
libidn	1.32-GNU-4.9.3-2.25
libjpeg-turbo	1.5.3-GCCcore-5.4.0
libpciaccess	0.13.4-intel-2016a
libpthread-stubs	0.3-intel-2016a
libsodium	1.0.8-foss-2016a
libtasn1	4.7-GNU-4.9.3-2.25
libtool	2.4.6-GCCcore-5.4.0
libunistring	0.9.3-GNU-4.9.3-2.25
libxcb	1.8-foss-2016a-Python-2.7.3
libxkbcommon	0.6.1-intel-2016a
libxslt	1.1.29-intel-2017a
libsndfile	1.0.28-GCCcore-6.4.0
libyaml	0.1.7-intel-2016a
libspatialindex	1.8.5-intel-2016a
libspatialite	4.3.0a-intel-2016a
LoFreq	2.1.2-intel-2017a-Python-2.7.12
LibUUID	1.0.3-foss-2016a
LAME	3.99.5-foss-2016b
LZO	2.10-foss-2016b
libgeotiff	1.4.2-foss-2018a
lua	5.3.4
lapack	gcc/64/3.8.0

[edit] M

Name	Latest version
MEGA2	4.9.1
Mathematica	10.3
manta	1.0.3
mat	test
matlab	R2019a
metasv	0.5.2
mriconvert	2.0.8
maskface	12272017
M4	1.4.18-GCCcore-5.4.0
MACH	1.0.18
MACS	1.4.2-1-goolf-1.7.20-Python-2.7.5
MOSAIK	2.2.28-intel-2016a-20140425-24cf06
MPICH	3.0.4-GCC-4.8.1
MRIcroGL	09302016
MRIcron	06_22_15
MRtrix	0.3.16-intel-2016a-Python-2.7.11
MUSCLE	3.8.31-intel-2016a
MVAPICH2	2.2b-GCC-4.9.3-2.25
Maq	0.7.0
Mathematica	11.0.1
Maven	3.3.9
Mercurial	3.2.4-foss-2015b-Python-2.7.9
Mesa	11.1.2-foss-2016b
Minimac2	2014.9.15-intel-2015b
Minimac3	1.0.10-intel-2015b
makedepend	1.0.5-foss-2016b
matplotlib	1.5.1-foss-2016a-Python-2.7.11
motif	2.3.7-intel-2016a
MACS2	2.1.1.20160309-foss-2016a-Python-2.7.11
MEME	4.12.0-foss-2016a
MultiQC	0.8~
Mono	5.2.0.224-intel-2017a
MaSuRCA	3.2.6-foss-2018a
minimap2	2.0rc1-foss-2016b
MotionCor2	1.0.5
mpich	ge/gcc/64/3.2.1
mpiexec	0.84_432
mvapich2	gcc/64/2.3b

[edit] N

Name	Latest version
NAMD	2.13b2-gpu
nccl	1.3.4-1
ncdu	1.13-20.1
nighres	1.1.0b1
NASM	2.13.03-GCCcore-5.4.0
NGS	1.2.5-foss-2016b
ncbi-vdb	2.7.0-foss-2016b
netCDF	4.6.0-foss-2018a
nodejs	4.4.7-foss-2016a
numactl	2.0.11-GCCcore-7.3.0
numpy	1.10.1-goolf-1.7.20-Python-2.7.11
NLopt	2.4.2-foss-2018a
NiBabel	2.1.0-intel-2017a-Python-2.7.13
ngmlr	0.2.6-foss-2016b
NCBI-Toolkit	18.0.0-intel-2017a
NCCL	2.2.13-CUDA-8.0.61
netcdf	gcc/64/4.5.0
netperf	2.7.0

[edit] O

Name	Latest version
openscenegraph	3.2.1
OTF	1.12.4-gompi-1.5.12
OpenPGM	5.2.122-intel-2015b
OpenSSL	1.0.2h-foss-2016b
OpenMM	6.3-intel-2016a-Python-2.7.11
openmpi	gcc/64/1.10.7
openblas	dynamic/0.2.20

[edit] P

Name	Latest version
parsync	1.69
PCRE	8.41-GCCcore-5.4.0
PDT	3.20-goolf-1.7.20
PETSc	3.6.3-intel-2015b-Python-2.7.11
PGI	18.5-GCC-6.4.0-2.28
PHASE	2.1.1
PIL	1.1.7-intel-2016a-Python-2.7.11
PROJ	5.0.0-foss-2018a
Pango	1.40.12-intel-2017a
Pindel	0.2.5b8-foss-2016b
ProbABEL	0.5.0
PyCairo	1.10.0-intel-2016a-Python-2.7.11
PyGObject	2.28.6-intel-2016a-Python-2.7.11
PyGTK	2.24.0-intel-2016a-Python-2.7.11
PyQt	4.11.4-intel-2016a-Python-2.7.11
PyZMQ	15.3.0-foss-2016a-Python-3.5.1-zmq4
Pygments	2.0.2-intel-2015b-Python-2.7.9
Pysam	0.9.1.4-foss-2016b-Python-2.7.12
p11-kit	0.23.2-GNU-4.9.3-2.25
parallel	20150822-GCC-4.9.2
path.py	8.2.1-foss-2016a-Python-3.5.1
perl-app-cpanminus	1.7039
pixman	0.34.0-GCCcore-5.4.0
pkgconfig	1.1.0-intel-2016a-Python-2.7.11
printproto	1.0.5-intel-2016a
prompt-toolkit	1.0.3-foss-2016a-Python-3.5.1
pysqlite	2.6.3-intel-2015b-Python-2.7.9
protobuf	3.3.0-intel-2017a
protobuf-python	3.3.0-intel-2017a-Python-3.6.1
PyYAML	3.12-intel-2016a-Python-3.5.1
prodigal	2.6.2-GCC-4.9.3-binutils-2.25
Pillow	4.3.0-intel-2017a-Python-2.7.13
p7zip	9.38.1
patchelf	0.9-foss-2016b
PCRE2	10.31-foss-2018a

[edit] Q

Name	Latest version
qdirstat	1.4
Qt	4.8.7-intel-2016a
Qwt	6.1.3-intel-2016a
QwtPolar	1.1.1-intel-2016a
QUAST	4.6.3-foss-2016a-Python-2.7.11
QIIME	qiime-dependencies
QWRAP	v3

[edit] R

Name	Latest version
RStudio	1.0.44
relion	2.1
rserver	3.5.2_X11
R	DESeq2.R-3.4.3-intel-2017a-X11-20170314
RAxML	8.1.1-goolf-1.4.10-mt-avx
RSeQC	2.6.3-goolf-1.7.20-Python-2.7.10-R-3.2.1
Ruby	2.3.3
randrproto	1.5.0-intel-2016a
renderproto	0.11-intel-2016a
requests	2.7.0-intel-2015b-Python-2.7.9
ResMap	1.1.4
RELION	2.1-intel-2016a-CUDA-8.0.44
Rust	1.30.1-foss-2016b

[edit] S

Name	Latest version
snakemakeslurm_local	4.8.0-1
SAS	v9.4
Salmon	0.7.2
soapsv	1.3
snakemake	4.8.0
sublime_text	3
S.A.G.E.	6.3
SCOTCH	6.0.4-intel-2015b
SHRiMP	2.2.3-goolf-1.4.10
SIP	4.18-intel-2016a-Python-2.7.11
SOLAR-Eclipse	8.1.1
SPAdes	3.12.0-foss-2016b
SPPARKS	07192016-intel-2016a
STAR-Fusion	0.8.0-goolf-1.4.10-Perl-5.16.3
STAR	2.5.2b~
SWIG	3.0.12-foss-2018a-Python-2.7.14
ScientificPython	2.9.4-intel-2015b-Python-2.7.11
Spack	0.10.0
scipy	0.17.0-intel-2016a-Python-2.7.11
shapeit	2.r837.GLIBCv2.12_linux_x86_64
sympy	0.7.6.1-intel-2015b-Python-2.7.11
SRA-Toolkit	2.8.2-1-centos_linux64
sparsehash	2.0.2-foss-2016a
Spark	2.2.0-Hadoop-2.6-Java-1.8.0_144
summovie	1.0.2
snakemakeslurm	4.8.0-1
scalapack	openmpi/gcc/64/2.0.2
sge	2011.11p1
slurm	17.11.8

[edit] T

Name	Latest version
tortoise	3.1.2
transdecoder	5.3.0
torch	7
tarquin	4.3.10
tcllib	1.19
Tar	1.29-goolf-1.4.10
Tk	8.6.8-foss-2018a
TopHat	2.1.1-foss-2016a
Trim_Galore	0.4.4-foss-2016b
Trimmomatic	0.36-Java-1.8.0_92
Trinity	2.2.0-foss-2016a
tabix	0.2.6-intel-2015b
tcsh	6.19.00-intel-2016a
testpath	0.3-foss-2016a-Python-3.5.1
texinfo	6.4-GCCcore-5.4.0
Tensorflow	1.2.0-intel-2017a-Python-3.6.1
TransDecoder	5.1.0-intel-2017a-Perl-5.24.1
trim_galore	0.4.2~
torque	6.1.1

[edit] U

Name	Latest version
unblur	1.0.2
usearch	7.0.1090

[edit] V

Name	Latest version
vmd	1.9.3
VEGAS	0.8.27
VICUNA	1.3
VPhaser-2	02112013-intel-2016a
VTK	6.3.0-foss-2016b-Python-2.7.12
VCFtools	0.1.15-intel-2016a-Perl-5.22.1

[edit] W

Name	Latest version
wcwidth	0.1.7-foss-2016a-Python-3.5.1
wxPython	3.0.2.0-intel-2017a-Python-2.7.13
wxWidgets	3.0.3-foss-2016b

[edit] X

Name	Latest version
xget	xget-public
XKeyboardConfig	2.17-intel-2016a
xbitmaps	1.1.1-intel-2016a
xcb-proto	1.7-foss-2016a-Python-2.7.3
xcb-util-image	0.4.0-intel-2016a
xcb-util-keysyms	0.4.0-intel-2016a
xcb-util-renderutil	0.3.9-intel-2016a
xcb-util-wm	0.4.1-intel-2016a
xcb-util	0.4.0-intel-2016a
xextproto	7.3.0-intel-2016a
xf86vidmodeproto	2.3.1-intel-2016a
xineramaproto	1.2.1-foss-2016b
xorg-macros	1.19.0-intel-2016a
xprop	1.2.2-foss-2016b
xproto	7.0.28-intel-2016a
xtrans	1.3.5-intel-2016a
Xerces-C++	3.1.2-intel-2015b
XQilla	2.3.2-intel-2015b
x264	20160614-foss-2016b
x265	2.4-foss-2016b

[edit] Y

Name	Latest version
Yasm	1.3.0-foss-2016b

[edit] Z

Name	Latest version
zlib	1.2.9-intel-2017a
ZeroMQ	4.1.4-foss-2016a

[edit] Software Detail

[edit] anvio

Available versions: 3

Command: module load rc/anvio

[edit] atom

Available versions: 1.30.0

Command: module load rc/atom

[edit] AFNI

Homepage: http://afni.nimh.nih.gov/

Description: AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data -a technique for mapping human brain activity.

Available versions: 17.1.08-intel-2016a-Python-2.7.11, dev-intel-2016a-Python-2.7.11, linux_openmp_64-goolf-1.7.20-20160616, 18.2.05-intel-2016a-Python-2.7.11

Command: module load AFNI

[edit] ANTs

Available versions: 2.1.0rc3-foss-2016a

Command: module load ANTs

[edit] APBS

Available versions: 1.4-linux-static-x86_64

Command: module load APBS

[edit] ASHS

Homepage: https://sites.google.com/site/hipposubfields/home

Description: Automatic Segmentation of Hippocampal Subfields (ASHS)

Available versions: rev103_20140612, 2.0.0_07202018

Command: module load ASHS

[edit] ATK

Homepage: https://developer.gnome.org/ATK/stable/

Description: ATK provides the set of accessibility interfaces that are implemented by othertoolkits and applications. Using the ATK interfaces, accessibility tools havefull access to view and control running applications.

Available versions: 2.18.0-intel-2016a, 2.26.0-intel-2017a

Command: module load ATK

[edit] ATLAS

Available versions: 3.10.1-gompi-1.5.12-LAPACK-3.4.2

Command: module load ATLAS

[edit] Amber

Available versions: 14-intel-2016a-AmberTools-15-patchlevel-13-13

Command: module load Amber

[edit] Anaconda2

Homepage: https://www.continuum.io/anaconda-overview}

Available versions: 4.0.0, 4.2.0

Command: module load Anaconda2

[edit] Aspera-Connect

Available versions: 3.6.1

Command: module load Aspera-Connect

[edit] AutoDock_Vina

Available versions: 1.1.2_linux_x86

Command: module load AutoDock_Vina

[edit] Autoconf

Homepage: http://www.gnu.org/software/autoconf/

Description: Autoconf is an extensible package of M4 macros that produce shell scriptsto automatically configure software source code packages. These scripts can adapt thepackages to many kinds of UNIX-like systems without manual user intervention. Autoconfcreates a configuration script for a package from a template file that lists theoperating system features that the package can use, in the form of M4 macro calls.

Available versions: 2.69, 2.69-GCC-4.8.4, 2.69-GCC-4.9.3-2.25, 2.69-GNU-4.9.3-2.25, 2.69-foss-2016a, 2.69-foss-2016b, 2.69-goolf-1.7.20, 2.69-intel-2015b, 2.69-intel-2016a, 2.69-GCCcore-6.3.0, 2.69-GCC-5.4.0-2.26, 2.69-intel-2017a, 2.69-GCCcore-6.4.0, 2.69-GCCcore-7.3.0, 2.69-GCCcore-5.4.0

Command: module load Autoconf

[edit] annovar

Available versions: 2016Feb01-foss-2015b-Perl-5.22.1

Command: module load annovar

[edit] ant

Available versions: 1.9.6-Java-1.7.0_80, 1.9.7-Java-1.8.0_92

Command: module load ant

[edit] ABySS

Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss

Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

Available versions: 1.9.0-foss-2016a, 2.0.2-foss-2016a

Command: module load ABySS

[edit] Anaconda3

Homepage: https://www.continuum.io/anaconda-overview

Description: Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platformthat empowers companies to adopt a modern open data science analytics architecture.

Available versions: 4.4.0, 5.0.1, 5.2.0, 5.1.0, 5.3.0

Command: module load Anaconda3

[edit] aaf-phylogeny

Available versions: 20160831

Command: module load aaf-phylogeny

[edit] acml

Available versions: gcc-int64/64/5.3.1, gcc-int64/fma4/5.3.1, gcc-int64/mp/64/5.3.1, gcc-int64/mp/fma4/5.3.1, gcc/64/5.3.1, gcc/fma4/5.3.1, gcc/mp/64/5.3.1, gcc/mp/fma4/5.3.1

Command: module load acml

[edit] BrainSuite

Available versions: 15b

Command: module load rc/BrainSuite

[edit] basespace-cli

Available versions: 0.8.12

Command: module load rc/basespace-cli

[edit] brainstorm

Available versions: 180709

Command: module load rc/brainstorm

[edit] BEDTools

Available versions: 2.26.0-foss-2016a

Command: module load BEDTools

[edit] BSMAP

Available versions: 2.90-foss-2016a

Command: module load BSMAP

[edit] BWA

Available versions: 0.7.13-intel-2015b, 0.7.13-intel-2016a

Command: module load BWA

[edit] BXH_XCEDE_TOOLS

Available versions: 1.11.1

Command: module load BXH_XCEDE_TOOLS

[edit] BamTools

Available versions: 2.4.0-goolf-1.7.20, 2.4.0-intel-2016a

Command: module load BamTools

[edit] Bismark

Homepage: http://www.bioinformatics.babraham.ac.uk/projects/bismark/

Description: A tool to map bisulfite converted sequence reads anddetermine cytosine methylation states

Available versions: 0.10.1-goolf-1.4.10, 0.18.0-foss-2016a, 0.18.0-goolf-1.4.10, 0.19.0-foss-2016a

Command: module load Bismark

[edit] Bowtie

Homepage: http://bowtie-bio.sourceforge.net/index.shtml}

Available versions: 1.1.1-goolf-1.4.10, 1.1.2-foss-2016a

Command: module load Bowtie

[edit] Bowtie2

Homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing readsto long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000sof characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Available versions: 2.0.2-foss-2016a, 2.0.2-goolf-1.4.10, 2.2.5-goolf-1.7.20, 2.2.6-intel-2015b, 2.2.8-foss-2016a, 2.3.3-intel-2017a

Command: module load Bowtie2

[edit] BreakDancer

Available versions: 1.4.5-intel-2016a

Command: module load BreakDancer

[edit] BCFtools

Homepage: http://www.htslib.org/

Description: Samtools is a suite of programs for interacting with high-throughput sequencing data.BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequencevariants

Available versions: 1.3.1-goolf-1.7.20, 1.6-intel-2016a

Command: module load BCFtools

[edit] BLAST+

Homepage: http://blast.ncbi.nlm.nih.gov/

Description: Basic Local Alignment Search Tool, or BLAST, is an algorithmfor comparing primary biological sequence information, such as the amino-acidsequences of different proteins or the nucleotides of DNA sequences.

Available versions: 2.6.0-intel-2017a-Python-2.7.13

Command: module load BLAST+

[edit] Biopython

Homepage: http://www.biopython.org

Description: Biopython is a set of freely available tools for biological computation writtenin Python by an international team of developers. It is a distributed collaborative effort todevelop Python libraries and applications which address the needs of current and future work inbioinformatics.

Available versions: 1.70-intel-2017a-Python-3.6.1

Command: module load Biopython

[edit] bioitx

Available versions: jupyter-0.7, jupyter-0.8, jupyter-1.0, jupyter

Command: module load bioitx

[edit] blacs

Available versions: openmpi/gcc/64/1.1patch03

Command: module load blacs

[edit] blas

Available versions: gcc/64/3.8.0

Command: module load blas

[edit] bonnie++

Available versions: 1.97.3

Command: module load bonnie++

[edit] cmg

Available versions: 2012.116.G, 2016.101.GU

Command: module load rc/cmg

[edit] cytoscape

Available versions: 2.8.2

Command: module load rc/cytoscape

[edit] cellranger

Available versions: 2.1.1, 2.2.0

Command: module load rc/cellranger

[edit] crossmap

Available versions: 0.2.8

Command: module load rc/crossmap

[edit] chezscheme

Available versions: 9.5

Command: module load rc/chezscheme

[edit] ceres

Available versions: 1.14.0, 1.13.0

Command: module load rc/ceres

[edit] CBLAS

Available versions: 20110120-foss-2016b

Command: module load CBLAS

[edit] CD-HIT

Homepage: http://weizhong-lab.ucsd.edu/cd-hit/

Description: CD-HIT is a very widely used program for clustering andcomparing protein or nucleotide sequences.

Available versions: 4.6.4-foss-2015b-2015-0603, 4.6.6-foss-2016b, 4.6.8-intel-2017a

Command: module load CD-HIT

[edit] CHARMM

Available versions: 40b1-intel-2016a

Command: module load CHARMM

[edit] CHASE

Available versions: v1

Command: module load CHASE

[edit] CUDA

Homepage: https://developer.nvidia.com/cuda-toolkit

Description: CUDA (formerly Compute Unified Device Architecture) is a parallelcomputing platform and programming model created by NVIDIA and implemented by thegraphics processing units (GPUs) that they produce. CUDA gives developers accessto the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.

Available versions: 7.5.18, 8.0.61_375.26-GCC-5.4.0-2.26, 8.0.61, 8.0.44, 9.2.148.1, 9.0.176, 9.2.88-GCC-7.3.0-2.30

Command: module load CUDA

[edit] Circos

Available versions: 0.69-5-intel-2016a-Perl-5.18.2

Command: module load Circos

[edit] ConnectomeWorkbench

Homepage: http://www.humanconnectome.org/software/connectome-workbench.html

Description: Connectome Workbench is an open-sourcevisualization and discovery tool used to explore data generatedby the Human Connectome Project. The distribution includes wb_view,a GUI-based visualization platform, and wb_command, a command-lineprogram for performing a variety of algorithmic tasks using volume,surface, and grayordinate data.

Available versions: 1.2.2, 1.3.1

Command: module load ConnectomeWorkbench

[edit] Cufflinks

Available versions: 2.2.1-foss-2016a, 2.2.1-goolf-1.7.20

Command: module load Cufflinks

[edit] cairo

Homepage: http://cairographics.org

Description: Cairo is a 2D graphics library with support for multiple output devices.Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers,PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB

Available versions: 1.14.6-intel-2015b, 1.14.6-intel-2016a, 1.14.6-intel-2016a-GLib-2.48.0, 1.14.8-intel-2017a, 1.14.10-GCCcore-6.3.0, 1.14.6-foss-2016b, 1.14.6-foss-2016b-GLib-2.48.0, 1.14.6-foss-2016a-GLib-2.48.0, 1.14.12-GCCcore-6.4.0

Command: module load cairo

[edit] configurable-http-proxy

Available versions: 1.3.0-foss-2016a-nodejs-4.4.7

Command: module load configurable-http-proxy

[edit] cutadapt

Available versions: 1.14-foss-2016b-Python-2.7.12, 1.9.1-foss-2016b-Python-2.7.12, 1.12

Command: module load cutadapt

[edit] CTFFIND

Homepage: http://grigoriefflab.janelia.org/ctf

Description: CTFFIND4 is a program for finding CTFs of electron micrographs.

Available versions: 4.1.8-intel-2016a, 4.1.8-foss-2016b

Command: module load CTFFIND

[edit] cuDNN

Homepage: https://developer.nvidia.com/cudnn

Description: The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives fordeep neural networks.

Available versions: 6.0-CUDA-8.0.61, 5.1-CUDA-8.0.61, 7.0.5-CUDA-9.0.176

Command: module load cuDNN

[edit] ctffind

Homepage: http://grigoriefflab.janelia.org/ctffind4

Description: program for finding CTFs of electron micrographs

Available versions: 4.0.17-foss-2016b

Command: module load ctffind

[edit] cluster-tools-dell

Available versions: 8.1

Command: module load cluster-tools-dell

[edit] cluster-tools

Available versions: 8.1

Command: module load cluster-tools

[edit] cuda90

Available versions: blas/9.0.176, fft/9.0.176, nsight/9.0.176, profiler/9.0.176, toolkit/9.0.176

Command: module load cuda90

[edit] cuda91

Available versions: blas/9.1.85, fft/9.1.85, nsight/9.1.85, profiler/9.1.85, toolkit/9.1.85

Command: module load cuda91

[edit] cuda80

Available versions: blas/8.0.61, fft/8.0.61, nsight/8.0.61, profiler/8.0.61, toolkit/8.0.61

Command: module load cuda80

[edit] cuda10.0

Available versions: blas/10.0.130, fft/10.0.130, nsight/10.0.130, profiler/10.0.130, toolkit/10.0.130

Command: module load cuda10.0

[edit] cuda92

Available versions: blas/9.2.88, fft/9.2.88, nsight/9.2.88, profiler/9.2.88, toolkit/9.2.88

Command: module load cuda92

[edit] delly

Available versions: 0.7.6

Command: module load rc/delly

[edit] dsistudio

Available versions: dsistudio-20151020

Command: module load rc/dsistudio

[edit] detonate

Available versions: 1.11

Command: module load rc/detonate

[edit] dicombrowser

Available versions: 1.7.0b5

Command: module load rc/dicombrowser

[edit] drracket

Available versions: 7.1

Command: module load rc/drracket

[edit] DBus

Homepage: http://dbus.freedesktop.org/doc/dbus-glib

Description: D-Bus is a message bus system, a simple way for applications to talkto one another. In addition to interprocess communication, D-Bus helpscoordinate process lifecycle; it makes it simple and reliable to codea "single instance" application or daemon, and to launch applicationsand daemons on demand when their services are needed.

Available versions: 1.10.8-intel-2016a, 1.11.20-intel-2017a

Command: module load DBus

[edit] DMTCP

Available versions: 2.4.5, 2.5.0

Command: module load DMTCP

[edit] Doxygen

Homepage: http://www.doxygen.org

Description: Doxygen is a documentation system for C++, C, Java, Objective-C, Python,IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to someextent D.

Available versions: 1.8.11-foss-2016a, 1.8.11-foss-2016b, 1.8.11-intel-2015b, 1.8.11-intel-2016a, 1.8.13-GCCcore-6.3.0, 1.8.13-GCCcore-6.4.0

Command: module load Doxygen

[edit] damageproto

Available versions: 1.2.1-foss-2016b, 1.2.1-goolf-1.7.20, 1.2.1-intel-2016a

Command: module load damageproto

[edit] dbus-glib

Homepage: http://dbus.freedesktop.org/doc/dbus-glib

Description: D-Bus is a message bus system, a simple way for applications to talk to one another.

Available versions: 0.106-intel-2016a, 0.108-intel-2017a

Command: module load dbus-glib

[edit] DB

Homepage: http://www.oracle.com/technetwork/products/berkeleydb

Description: Berkeley DB enables the development of custom data management solutions,without the overhead traditionally associated with such custom projects.

Available versions: 6.0.30-foss-2016a, 6.2.32-intel-2017a

Command: module load DB

[edit] dvctools

Available versions: 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.2, 1.0, latest, recommended

Command: module load dvctools

[edit] EMAN2

Available versions: 2.2

Command: module load rc/EMAN2

[edit] EIGENSOFT

Homepage: http://www.hsph.harvard.edu/alkes-price/software/

Description: The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al.2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principalcomponents analysis to explicitly model ancestry differences between cases and controls along continuous axes ofvariation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestralpopulations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFTpackage has a built-in plotting script and supports multiple file formats and quantitative phenotypes.

Available versions: 6.1.1-goolf-1.7.20, 6.1.4-foss-2016b

Command: module load EIGENSOFT

[edit] ENT

Available versions: 1.0.2

Command: module load ENT

[edit] EPACTS

Available versions: 3.2.6-foss-2016b

Command: module load EPACTS

[edit] Elk

Homepage: http://elk.sourceforge.net/}

Available versions: 4.0.15-intel-2016a, 4.3.6-intel-2016a

Command: module load Elk

[edit] Emacs

Available versions: 24.5-GCC-4.9.3-2.25

Command: module load Emacs

[edit] entrypoints

Available versions: 0.2.2-foss-2016a-Python-3.5.1

Command: module load entrypoints

[edit] eudev

Homepage: https://wiki.gentoo.org/wiki/Project:Eudev

Description: eudev is a fork of systemd-udev with the goal of obtainingbetter compatibility with existing software such asOpenRC and Upstart, older kernels, various toolchainsand anything else required by users and various distributions.

Available versions: 3.1.5-goolf-1.7.20, 3.1.5-intel-2016a, 3.1.5-foss-2016b

Command: module load eudev

[edit] EDGE_pro

Homepage: http://ccb.jhu.edu/software/EDGE-pro/

Description: EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes)is an efficient software system to estimate gene expression levels inprokaryotic genomes from RNA-seq data. EDGE-pro uses Bowtie2 for alignmentand then estimates expression directly from the alignment results.

Available versions: 1.3.1

Command: module load EDGE_pro

[edit] exonerate

Available versions: 2.2.0

Command: module load exonerate

[edit] EDGE_pro_patch

Homepage: http://ccb.jhu.edu/software/EDGE-pro/

Description: EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes)is an efficient software system to estimate gene expression levels inprokaryotic genomes from RNA-seq data. EDGE-pro uses Bowtie2 for alignmentand then estimates expression directly from the alignment results.

Available versions: 1.3.1-2

Command: module load EDGE_pro_patch

[edit] FSL

Homepage: http://www.fmrib.ox.ac.uk/fsl/

Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Available versions: 5.0.9-Modified-fsl_sub, 6.0.0

Command: module load rc/FSL

[edit] fdtd

Available versions: 8.17.1157-1

Command: module load rc/fdtd

[edit] freesurfer

Available versions: freesurfer-5.3.0, freesurfer-5.3.0-HCP, Dev/10_29_16

Command: module load rc/freesurfer

[edit] fpart

Available versions: 1.1.0

Command: module load rc/fpart

[edit] freeimage

Available versions: 3.18

Command: module load rc/freeimage

[edit] FASTX-Toolkit

Available versions: 0.0.14-intel-2015b

Command: module load FASTX-Toolkit

[edit] FIAT

Available versions: 1.6.0-intel-2015b-Python-2.7.11

Command: module load FIAT

[edit] FLTK

Homepage: http://www.fltk.org

Description: FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows,and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGLand its built-in GLUT emulation.

Available versions: 1.3.3-intel-2016a, 1.3.3-foss-2016b

Command: module load FLTK

[edit] FLUENT

Homepage: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent

Description: ANSYS FLUENT software contains the broad physical modeling capabilities neededto model flow, turbulence, heat transfer, and reactions for industrial applications ranging fromair flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms,from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.

Available versions: 18.0, 19.1

Command: module load FLUENT

[edit] FSL

Homepage: http://www.fmrib.ox.ac.uk/fsl/

Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Available versions: 5.0.9-centos6_64, 6.0.0-intel-2017a, 5.0.10-intel-2017a

Command: module load FSL

[edit] FastQC

Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Description: FastQC is a quality control application for high throughput sequence data.It reads in sequence data in a variety of formats and can either provide an interactiveapplication to review the results of several different QC checks, or create an HTML basedreport which can be integrated into a pipeline.

Available versions: 0.11.5-Java-1.7.0_80, 0.11.5-Java-1.8.0_74, 0.11.7-Java-1.8.0_74

Command: module load FastQC

[edit] FastTree

Available versions: 2.1.7-goolf-1.4.10, 2.1.9-goolf-1.4.10

Command: module load FastTree

[edit] FreeSurfer

Available versions: 5.3.0-centos6_x86_64, 6.0.0-centos6_x86_64

Command: module load FreeSurfer

[edit] fastPHASE

Available versions: 1.4.8

Command: module load fastPHASE

[edit] file

Available versions: 5.28-foss-2016b

Command: module load file

[edit] fixesproto

Homepage: http://www.freedesktop.org/wiki/Software/xlibs

Description: X.org FixesProto protocol headers.

Available versions: 5.0-foss-2016b, 5.0-goolf-1.7.20, 5.0-intel-2015b, 5.0-intel-2016a, 5.0-foss-2016a

Command: module load fixesproto

[edit] flex

Homepage: http://flex.sourceforge.net/

Description: Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner,sometimes called a tokenizer, is a program which recognizes lexical patterns in text.

Available versions: 2.5.35-foss-2016a, 2.5.39, 2.5.39-GCC-4.9.3-binutils-2.25, 2.5.39-GCCcore-4.9.3, 2.5.39-intel-2015b, 2.6.0, 2.6.0-GCCcore-5.4.0, 2.6.0-foss-2016a, 2.6.0-foss-2016b, 2.6.0-goolf-1.7.20, 2.6.0-intel-2015b, 2.6.0-intel-2016a, 2.6.3-GCCcore-6.3.0, 2.6.0-GCCcore-6.1.0, 2.6.4-GCCcore-6.3.0, 2.6.3, 2.6.4-GCCcore-6.4.0, 2.5.39-intel-2016a, 2.6.0-intel-2017a, 2.6.4, 2.6.4-GCCcore-7.3.0, 2.6.3-GCCcore-5.4.0, 2.6.4-GCCcore-5.4.0, 2.6.3-GCCcore-7.3.0

Command: module load flex

[edit] fontsproto

Available versions: 2.1.3-foss-2016b, 2.1.3-goolf-1.7.20, 2.1.3-intel-2016a

Command: module load fontsproto

[edit] freeglut

Homepage: http://freeglut.sourceforge.net/

Description: freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.

Available versions: 3.0.0-foss-2016b, 3.0.0-intel-2016a, 3.0.0-intel-2017a

Command: module load freeglut

[edit] FastQ_Screen

Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

Description: FastQ Screen allows you to set up a standard set of librariesagainst which all of your sequences can be searched. Your search libraries mightcontain the genomes of all of the organisms you work on, along with PhiX,Vectors or other contaminants commonly seen in sequencing experiments.

Available versions: 0.11.2

Command: module load FastQ_Screen

[edit] Firefox

Homepage: https://www.mozilla.org/en-US/firefox/new/

Description: Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on theMozilla code base and offers customization options and features such as its capability to block pop-up windows,tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.

Available versions: 44.0.2

Command: module load Firefox

[edit] FreeXL

Homepage: https://www.gaia-gis.it/fossil/freexl/index

Description: FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.

Available versions: 1.0.2-foss-2016b, 1.0.2-intel-2016a

Command: module load FreeXL

[edit] freebayes

Homepage: https://github.com/ekg/freebayes

Description: Bayesian haplotype-based polymorphism discovery and genotyping.

Available versions: 1.1.0-goolf-1.7.20_39e5e4b

Command: module load freebayes

[edit] frealign

Homepage: http://grigoriefflab.janelia.org/frealign

Description: Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images ofsingle particles.

Available versions: 9.11-intel-2016a-avx-mp

Command: module load frealign

[edit] FriBidi

Homepage: https://directory.fsf.org/wiki/Fribidi

Description: FriBidi is a free implementation of the Unicode Bidirectional (BiDi) Algorithm. It also providesutility functions to aid in the development of interactive editors and widgets that implement BiDi functionality.The BiDi algorithm is a prerequisite for supporting right-to-left scripts such as Hebrew, Arabic, Syriac, andThaana.

Available versions: 1.0.1-foss-2016b

Command: module load FriBidi

[edit] freeipmi

Available versions: 1.5.7

Command: module load freeipmi

[edit] fftw2

Available versions: openmpi/gcc/64/double/2.1.5, openmpi/gcc/64/float/2.1.5

Command: module load fftw2

[edit] fftw3

Available versions: openmpi/gcc/64/3.3.7

Command: module load fftw3

[edit] GEMMA

Available versions: GEMMA_Rec

Command: module load rc/GEMMA

[edit] gromacs-intel

Available versions: 5.1.1, 2018.1

Command: module load rc/gromacs-intel

[edit] GeneTorrent

Available versions: GeneTorrent_4.0.0-9

Command: module load rc/GeneTorrent

[edit] GATK

Available versions: 3.7-Java-1.8.0_112, 3.7-Java-1.8.0_92

Command: module load GATK

[edit] GC3Pie

Available versions: 2.4.2

Command: module load GC3Pie

[edit] GCC

Homepage: http://gcc.gnu.org/

Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,as well as libraries for these languages (libstdc++, libgcj,...).

Available versions: 4.7.2, 4.8.1, 4.8.2, 4.8.4, 4.9.2, 4.9.3, 4.9.3-2.25, 4.9.3-binutils-2.25, 5.4.0-2.26, system, 6.1.0-2.27, 6.3.0-2.27, 6.4.0-2.28, 4.4.7, 7.3.0-2.30

Command: module load GCC

[edit] GCCcore

Homepage: http://gcc.gnu.org/

Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,as well as libraries for these languages (libstdc++, libgcj,...).

Available versions: 4.9.3, 5.4.0, 6.3.0, 6.1.0, 6.4.0, 7.3.0

Command: module load GCCcore

[edit] GD

Available versions: 2.52-intel-2016a-Perl-5.18.2

Command: module load GD

[edit] GDAL

Homepage: http://www.gdal.org/

Description: GDAL is a translator library for raster geospatial data formats that is released under an X/MIT styleOpen Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data modelto the calling application for all supported formats. It also comes with a variety of useful commandline utilities fordata translation and processing.

Available versions: 2.0.2-intel-2016a, 2.1.0-foss-2016a, 2.1.0-foss-2016b, 2.1.0-intel-2015b, 2.1.0-intel-2016a, 2.1.3-intel-2017a-Python-2.7.13, 2.1.3-foss-2016b-Python-2.7.12, 2.1.3-intel-2016a-Python-2.7.12, 2.2.3-foss-2018a-Python-3.6.4

Command: module load GDAL

[edit] GNU

Available versions: 4.9.3-2.25

Command: module load GNU

[edit] GObject-Introspection

Homepage: https://wiki.gnome.org/GObjectIntrospection/

Description: GObject introspection is a middleware layer between C libraries(using GObject) and language bindings. The C library can be scanned atcompile time and generate a metadata file, in addition to the actualnative C library. Then at runtime, language bindings can read thismetadata and automatically provide bindings to call into the C library.

Available versions: 1.47.1-foss-2016b, 1.47.1-intel-2016a, 1.48.0-intel-2016a, 1.53.5-intel-2017a-Python-2.7.13, 1.48.0-foss-2016b, 1.48.0-foss-2016a

Command: module load GObject-Introspection

[edit] GTK+

Homepage: https://developer.gnome.org/gtk+/stable/

Description: The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.

Available versions: 2.24.28-intel-2016a, 2.24.31-intel-2017a

Command: module load GTK+

[edit] Gdk-Pixbuf

Homepage: https://developer.gnome.org/gdk-pixbuf/stable/

Description: The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation.It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past itwas distributed as part of GTK+ 2 but it was split off into a separate packagein preparation for the change to GTK+ 3.

Available versions: 2.32.3-intel-2016a, 2.36.10-intel-2017a

Command: module load Gdk-Pixbuf

[edit] gawk

Available versions: 4.0.2-goolf-1.4.10

Command: module load gawk

[edit] gcccuda

Homepage: (none)

Description: GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.

Available versions: 2017.01, 2018b

Command: module load gcccuda

[edit] glproto

Homepage: http://www.freedesktop.org/wiki/Software/xlibs

Description: X protocol and ancillary headers

Available versions: 1.4.17-intel-2016a, 1.4.17-foss-2016b

Command: module load glproto

[edit] gnuplot

Available versions: 5.0.3-foss-2016b, 5.0.3-intel-2016a

Command: module load gnuplot

[edit] gnutls

Available versions: 3.4.7-GNU-4.9.3-2.25

Command: module load gnutls

[edit] goolf

Available versions: 1.4.10, 1.7.20

Command: module load goolf

[edit] grep

Available versions: 2.15-goolf-1.4.10

Command: module load grep

[edit] groff

Available versions: 1.22.2, 1.22.2-foss-2016b

Command: module load groff

[edit] gtool

Available versions: 0.7.5_linux_x86_64

Command: module load gtool

[edit] guile

Available versions: 1.8.8-GNU-4.9.3-2.25

Command: module load guile

[edit] GEOS

Homepage: http://trac.osgeo.org/geos

Description: GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)

Available versions: 3.6.1-intel-2017a-Python-2.7.13, 3.6.1-foss-2016b-Python-2.7.12, 3.6.1-intel-2016a-Python-2.7.12, 3.6.2-foss-2018a-Python-3.6.4

Command: module load GEOS

[edit] GStreamer

Homepage: http://gstreamer.freedesktop.org/

Description: GStreamer is a library for constructing graphs of media-handlingcomponents. The applications it supports range from simpleOgg/Vorbis playback, audio/video streaming to complex audio(mixing) and video (non-linear editing) processing.

Available versions: 0.10.36-intel-2017a, 1.8.3-foss-2016b, 1.8.3-foss-2016a

Command: module load GStreamer

[edit] GConf

Homepage: https://projects.gnome.org/gconf/

Description: GConf is a system for storing application preferences.It is intended for user preferences; not configurationof something like Apache, or arbitrary data storage.

Available versions: 3.2.6-intel-2017a

Command: module load GConf

[edit] GST-plugins-base

Homepage: http://gstreamer.freedesktop.org/

Description: GStreamer is a library for constructing graphs of media-handlingcomponents. The applications it supports range from simpleOgg/Vorbis playback, audio/video streaming to complex audio(mixing) and video (non-linear editing) processing.

Available versions: 0.10.36-intel-2017a

Command: module load GST-plugins-base

[edit] gdc-client

Homepage: https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool

Description: The gdc-client provides several convenience functions over the GDC API which provides generaldownload/upload via HTTPS.

Available versions: 1.0.1-intel-2016a-Python-2.7.12, 1.3.0-intel-2016a-Python-2.7.12

Command: module load gdc-client

[edit] Gctf

Homepage: https://www.mrc-lmb.cam.ac.uk/kzhang/

Description: Gctf is a tool for real-time CTF determination and correction.

Available versions: 1.06, 1.06_devel

Command: module load Gctf

[edit] gzip

Homepage: http://www.gnu.org/software/gzip/

Description: gzip (GNU zip) is a popular data compression program as a replacement for compress

Available versions: 1.8-GCCcore-6.3.0, 1.6

Command: module load gzip

[edit] gcc

Available versions: 7.2.0

Command: module load gcc

[edit] gdb

Available versions: 8.0.1

Command: module load gdb

[edit] globalarrays

Available versions: openmpi/gcc/64/5.6.1

Command: module load globalarrays

[edit] hydrasv

Available versions: 0.5.3

Command: module load rc/hydrasv

[edit] HOMER

Available versions: 4.9

Command: module load rc/HOMER

[edit] HAPGEN2

Available versions: 2.2.0

Command: module load HAPGEN2

[edit] HISAT2

Available versions: 2.1.0-foss-2016b

Command: module load HISAT2

[edit] HPL

Available versions: 2.1-intel-2016a, 2.2-intel-2016a

Command: module load HPL

[edit] HTSeq

Available versions: 0.6.1p1-foss-2016b-Python-2.7.12, 0.6.1p1-intel-2015b-Python-2.7.8

Command: module load HTSeq

[edit] HarfBuzz

Homepage: http://www.freedesktop.org/wiki/Software/HarfBuzz

Description: HarfBuzz is an OpenType text shaping engine.

Available versions: 1.1.3-foss-2016b, 1.1.3-intel-2016a, 1.2.7-intel-2016a, 1.5.1-intel-2017a

Command: module load HarfBuzz

[edit] Hypre

Available versions: 2.10.1-intel-2015b

Command: module load Hypre

[edit] h5py

Available versions: 2.5.0-intel-2016a-Python-2.7.11-HDF5-1.8.16

Command: module load h5py

[edit] help2man

Homepage: https://www.gnu.org/software/help2man/

Description: help2man produces simple manual pages from the '--help' and '--version' output of other commands.

Available versions: 1.47.4-GCCcore-6.3.0, 1.47.4, 1.47.4-GCCcore-6.4.0, 1.47.4-GCCcore-7.3.0, 1.47.4-GCCcore-5.4.0

Command: module load help2man

[edit] hwloc

Available versions: 1.10.1-GCC-4.8.4, 1.11.0-GNU-4.9.3-2.25, 1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25, 1.11.2-GCC-4.9.3-2.25, 1.11.3-GCC-5.4.0-2.26, 1.11.5-GCC-5.4.0-2.26, 1.6.2-GCC-4.7.2, 1.8.1-GCC-4.8.2, 1.11.3-intel-2017a, 1.11.3-GCC-6.1.0-2.27, 1.11.5-GCC-6.3.0-2.27, 1.11.8-GCCcore-6.4.0, 1.11.3-intel-2016a, 1.11.10-GCCcore-7.3.0, 1.11.8

Command: module load hwloc

[edit] HMMER

Homepage: http://hmmer.org/

Description: HMMER is used for searching sequence databases for homologs of protein sequences,and for making protein sequence alignments. It implements methods using probabilistic modelscalled profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and othersequence alignment and database search tools based on older scoring methodology,HMMER aims to be significantly more accurate and more able to detect remote homologsbecause of the strength of its underlying mathematical models. In the past, this strengthcame at significant computational expense, but in the new HMMER3 project, HMMER is nowessentially as fast as BLAST.

Available versions: 3.1b2-intel-2016a

Command: module load HMMER

[edit] hdf5

Available versions: 1.10.1

Command: module load hdf5

[edit] hdf5_18

Available versions: 1.8.20

Command: module load hdf5_18

[edit] hpl

Available versions: 2.2

Command: module load hpl

[edit] intel

Available versions: compiler/64/ps_2016/2016.0.047

Command: module load rc/intel

[edit] IMPUTE2

Available versions: 2.3.0_x86_64_static, 2.3.2_x86_64_static

Command: module load IMPUTE2

[edit] IPython

Available versions: 3.2.0-intel-2015b-Python-2.7.9, 5.0.0-foss-2016a-Python-3.5.1

Command: module load IPython

[edit] icc

Homepage: http://software.intel.com/en-us/intel-compilers/

Description: C and C++ compiler from Intel

Available versions: 2015.3.187, 2015.3.187-GNU-4.9.3-2.25, 2016.1.150-GCC-4.9.3-2.25, 2017.1.132-GCC-6.3.0-2.27, 2017.4.196-GCC-6.4.0-2.28, 2016.3.210-GCC-5.4.0-2.26

Command: module load icc

[edit] iccifort

Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI andIntel MKL

Available versions: 2015.3.187-GNU-4.9.3-2.25, 2016.1.150-GCC-4.9.3-2.25, 2017.1.132-GCC-6.3.0-2.27, 2017.4.196-GCC-6.4.0-2.28, 2016.3.210-GCC-5.4.0-2.26

Command: module load iccifort

[edit] ifort

Homepage: http://software.intel.com/en-us/intel-compilers/

Description: Fortran compiler from Intel

Available versions: 2015.3.187-GNU-4.9.3-2.25, 2016.1.150-GCC-4.9.3-2.25, 2017.1.132-GCC-6.3.0-2.27, 2017.4.196-GCC-6.4.0-2.28, 2016.3.210-GCC-5.4.0-2.26

Command: module load ifort

[edit] iimpi

Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

Description: Intel C/C++ and Fortran compilers, alongside Intel MPI.

Available versions: 7.3.5-GNU-4.9.3-2.25, 8.1.5-GCC-4.9.3-2.25, 2017a, 2016b

Command: module load iimpi

[edit] imkl

Homepage: http://software.intel.com/en-us/intel-mkl/

Description: Intel Math Kernel Library is a library of highly optimized,extensively threaded math routines for science, engineering, and financialapplications that require maximum performance. Core math functions includeBLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.

Available versions: 11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25, 11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25, 2017.1.132-iimpi-2017a, 11.3.3.210-iimpi-2016b

Command: module load imkl

[edit] impi

Homepage: http://software.intel.com/en-us/intel-mpi-library/

Description: The Intel(R) MPI Library for Linux* OS is a multi-fabric messagepassing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library forLinux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.

Available versions: 5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25, 5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25, 2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27, 5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26

Command: module load impi

[edit] inputproto

Available versions: 2.3-foss-2016a, 2.3.1-foss-2015b, 2.3.1-foss-2016a, 2.3.1-foss-2016b, 2.3.1-goolf-1.7.20, 2.3.1-intel-2015b, 2.3.1-intel-2016a

Command: module load inputproto

[edit] intel

Available versions: 2015b, 2016a, 2017a, 2016b, mic/sdk/3.8.4

Command: module load intel

[edit] ITK

Homepage: https://itk.org

Description: Insight Segmentation and Registration Toolkit (ITK) providesan extensive suite of software tools for registering and segmentingmultidimensional imaging data.

Available versions: 4.12.2-foss-2016b-Python-2.7.12

Command: module load ITK

[edit] ICU

Homepage: http://site.icu-project.org/home

Description: ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalizationsupport for software applications.

Available versions: 61.1-GCCcore-6.4.0

Command: module load ICU

[edit] ipmitool

Available versions: 1.8.18

Command: module load ipmitool

[edit] intel-tbb-oss

Available versions: ia32/2018_20180618oss, intel64/2018_20180618oss

Command: module load intel-tbb-oss

[edit] iozone

Available versions: 3_471

Command: module load iozone

[edit] jspr

Available versions: 2017-7-20

Command: module load rc/jspr

[edit] JAGS

Available versions: 3.4.0-goolf-1.4.10

Command: module load JAGS

[edit] JUnit

Available versions: 4.12-Java-1.7.0_80, 4.12-Java-1.8.0_92

Command: module load JUnit

[edit] Java

Available versions: 1.7.0_10, 1.7.0_15, 1.7.0_21, 1.7.0_80, 1.8.0_112, 1.8.0_25, 1.8.0_45, 1.8.0_60, 1.8.0_72, 1.8.0_74, 1.8.0_92, 1.8.0_121, 1.8.0_144, 1.8.0_141, 1.8.0_152, 1.8.0_162, .modulerc

Command: module load Java

[edit] Jellyfish

Homepage: http://www.genome.umd.edu/jellyfish.html

Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

Available versions: 2.2.4-intel-2015b, 2.2.6-foss-2016b

Command: module load Jellyfish

[edit] jupyterhub

Available versions: 0.6.1-foss-2016a-Python-3.5.1

Command: module load jupyterhub

[edit] Kent_tools

Available versions: 340

Command: module load Kent_tools

[edit] Kerberos_V5

Available versions: 1.12.2-intel-2015b

Command: module load Kerberos_V5

[edit] kbproto

Available versions: 1.0.6-foss-2015b, 1.0.6-foss-2016a, 1.0.6-goolf-1.7.20, 1.0.6-intel-2016a, 1.0.7-foss-2016a, 1.0.7-foss-2016b, 1.0.7-goolf-1.7.20, 1.0.7-intel-2015b, 1.0.7-intel-2016a

Command: module load kbproto

[edit] KING

Homepage: http://people.virginia.edu/~wc9c/KING/

Description: KING is a toolset making use of high-throughput SNPdata typically seen in a genome-wide association study (GWAS) or asequencing project. Applications of KING include family relationshipinference and pedigree error checking, population substructureidentification, forensics, gene mapping, etc.

Available versions: 2.1.2-foss-2016a

Command: module load KING

[edit] kallisto

Homepage: http://pachterlab.github.io/kallisto/

Description: kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generallyof target sequences using high-throughput sequencing reads.

Available versions: 0.43.1-intel-2017a

Command: module load kallisto

[edit] lstc

Available versions: lsdyna

Command: module load rc/lstc

[edit] lumpy

Available versions: 0.2.13

Command: module load rc/lumpy

[edit] lcmodel

Available versions: 6.3

Command: module load rc/lcmodel

[edit] luajit

Available versions: 2.0.5

Command: module load rc/luajit

[edit] libarchive

Available versions: 3.1.2-10

Command: module load rc/libarchive

[edit] LAPACK

Available versions: 3.4.2-gompi-1.5.12

Command: module load LAPACK

[edit] LeadIT

Available versions: 2.1.9

Command: module load LeadIT

[edit] LibTIFF

Homepage: http://www.remotesensing.org/libtiff/

Description: tiff: Library and tools for reading and writing TIFF data files

Available versions: 4.0.3-foss-2016b, 4.0.4-goolf-1.7.20, 4.0.4-intel-2015b, 4.0.6-foss-2016b, 4.0.6-intel-2015b, 4.0.6-intel-2016a, 4.0.7-intel-2017a, 4.0.8-intel-2017a, 3.9.7-intel-2016a, 4.0.6-intel-2016b, 4.0.9-GCCcore-6.4.0, 4.0.7-foss-2016b, 4.0.9-GCCcore-5.4.0

Command: module load LibTIFF

[edit] Lmod

Available versions: 6.3-GCC-4.8.4

Command: module load Lmod

[edit] LocusZoom

Available versions: 1.3-goolf-1.7.20

Command: module load LocusZoom

[edit] Lua

Available versions: 5.1.4-8-GCC-4.8.4

Command: module load Lua

[edit] lftp

Available versions: 4.6.4-GNU-4.9.3-2.25

Command: module load lftp

[edit] libGLU

Homepage: ftp://ftp.freedesktop.org/pub/mesa/glu/

Description: The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.

Available versions: 9.0.0-foss-2016b, 9.0.0-intel-2016a, 9.0.0-intel-2016a-Mesa-11.2.1, 9.0.0-intel-2017a, 9.0.0-foss-2018a

Command: module load libGLU

[edit] libICE

Available versions: 1.0.8-foss-2016a, 1.0.8-intel-2016a, 1.0.9-foss-2016a, 1.0.9-foss-2016b, 1.0.9-intel-2015b, 1.0.9-intel-2016a

Command: module load libICE

[edit] libSM

Available versions: 1.2.1-foss-2016a, 1.2.1-intel-2016a, 1.2.2-foss-2016a, 1.2.2-foss-2016b, 1.2.2-intel-2015b, 1.2.2-intel-2016a

Command: module load libSM

[edit] libX11

Available versions: 1.6.1-foss-2016a, 1.6.3-foss-2016a, 1.6.3-foss-2016b, 1.6.3-goolf-1.7.20, 1.6.3-goolf-1.7.20-Python-2.7.9, 1.6.3-intel-2015b, 1.6.3-intel-2015b-Python-2.7.10, 1.6.3-intel-2016a

Command: module load libX11

[edit] libXau

Available versions: 1.0.8-foss-2015b, 1.0.8-foss-2016a, 1.0.8-foss-2016b, 1.0.8-goolf-1.7.20, 1.0.8-intel-2015b, 1.0.8-intel-2016a

Command: module load libXau

[edit] libXcursor

Homepage: http://www.freedesktop.org/wiki/Software/xlibs

Description: X Cursor management library

Available versions: 1.1.14-intel-2016a, 1.1.14-foss-2016b

Command: module load libXcursor

[edit] libXdamage

Available versions: 1.1.4-foss-2016b, 1.1.4-goolf-1.7.20, 1.1.4-intel-2016a

Command: module load libXdamage

[edit] libXdmcp

Homepage: http://www.freedesktop.org/wiki/Software/xlibs}

Available versions: 1.1.1-intel-2016a, 1.1.2-foss-2015b, 1.1.2-foss-2016a, 1.1.2-foss-2016b, 1.1.2-goolf-1.7.20, 1.1.2-intel-2015b, 1.1.2-intel-2016a

Command: module load libXdmcp

[edit] libXext

Available versions: 1.3.3-foss-2016a, 1.3.3-foss-2016b, 1.3.3-goolf-1.7.20, 1.3.3-intel-2015b, 1.3.3-intel-2016a

Command: module load libXext

[edit] libXfixes

Available versions: 5.0.1-foss-2016b, 5.0.1-goolf-1.7.20, 5.0.1-intel-2015b, 5.0.1-intel-2016a

Command: module load libXfixes

[edit] libXfont

Available versions: 1.5.1-foss-2016b, 1.5.1-goolf-1.7.20, 1.5.1-intel-2016a, 1.5.1-intel-2016a-freetype-2.6.3

Command: module load libXfont

[edit] libXft

Homepage: http://www.freedesktop.org/wiki/Software/xlibs

Description: X11 client-side library

Available versions: 2.3.2-foss-2016a, 2.3.2-intel-2016a, 2.3.2-foss-2016b

Command: module load libXft

[edit] libXi

Available versions: 1.7.4-intel-2015b, 1.7.6-goolf-1.7.20, 1.7.6-intel-2016a

Command: module load libXi

[edit] libXinerama

Homepage: http://www.freedesktop.org/wiki/Software/xlibs

Description: Xinerama multiple monitor library

Available versions: 1.1.3-intel-2016a, 1.1.3-foss-2016b

Command: module load libXinerama

[edit] libXmu

Available versions: 1.1.2-foss-2016a, 1.1.2-intel-2016a

Command: module load libXmu

[edit] libXp

Available versions: 1.0.3-foss-2016a, 1.0.3-goolf-1.7.20, 1.0.3-intel-2016a

Command: module load libXp

[edit] libXpm

Available versions: 3.5.11-foss-2016a, 3.5.11-intel-2016a

Command: module load libXpm

[edit] libXrandr

Available versions: 1.5.0-goolf-1.7.20, 1.5.0-intel-2016a

Command: module load libXrandr

[edit] libXrender

Available versions: 0.9.9-foss-2016a, 0.9.9-foss-2016b, 0.9.9-goolf-1.7.20, 0.9.9-intel-2015b, 0.9.9-intel-2016a

Command: module load libXrender

[edit] libXt

Available versions: 1.1.4-foss-2016a, 1.1.5-foss-2016a, 1.1.5-foss-2016b, 1.1.5-intel-2015b, 1.1.5-intel-2016a

Command: module load libXt

[edit] libcerf

Available versions: 1.4-foss-2016b, 1.4-intel-2016a

Command: module load libcerf

[edit] libdrm

Homepage: http://dri.freedesktop.org

Description: Direct Rendering Manager runtime library.

Available versions: 2.4.67-foss-2016b, 2.4.67-goolf-1.7.20, 2.4.67-intel-2016a, 2.4.68-intel-2016a, 2.4.70-foss-2016b, 2.4.76-intel-2017a, 2.4.88-GCCcore-6.4.0, 2.4.91-GCCcore-6.4.0, 2.4.91-GCCcore-5.4.0

Command: module load libdrm

[edit] libfontenc

Available versions: 1.1.3-foss-2016b, 1.1.3-goolf-1.7.20, 1.1.3-intel-2016a

Command: module load libfontenc

[edit] libgcrypt

Homepage: https://gnupg.org/related_software/libgcrypt/index.html

Description: Libgpg-error is a small library that defines common error values for all GnuPG components.

Available versions: 1.6.5-intel-2016a, 1.6.5-foss-2016a, 1.6.5-intel-2017a

Command: module load libgcrypt

[edit] libgd

Homepage: https://libgd.github.io/

Description: GD is an open source code library for the dynamic creation of images by programmers.

Available versions: 2.1.0-intel-2016a, 2.1.1-foss-2016b, 2.1.1-intel-2016a, 2.2.3-intel-2016a, 2.2.4-intel-2017a

Command: module load libgd

[edit] libglade

Available versions: 2.6.4-intel-2016a

Command: module load libglade

[edit] libgpg-error

Homepage: https://gnupg.org/related_software/libgpg-error/index.html

Description: Libgpg-error is a small library that defines common error values for all GnuPG components.

Available versions: 1.21-intel-2016a, 1.21-foss-2016a, 1.21-foss-2016b, 1.21-intel-2017a

Command: module load libgpg-error

[edit] libgtextutils

Available versions: 0.6.1-intel-2015b

Command: module load libgtextutils

[edit] libidn

Available versions: 1.32-GNU-4.9.3-2.25

Command: module load libidn

[edit] libjpeg-turbo

Homepage: http://sourceforge.net/projects/libjpeg-turbo/

Description: libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD toaccelerate baseline JPEG compression and decompression. libjpeg is a librarythat implements JPEG image encoding, decoding and transcoding.

Available versions: 1.3.1-intel-2016a, 1.4.0-goolf-1.7.20, 1.4.1-foss-2015b, 1.4.2-foss-2016a, 1.4.2-foss-2016b, 1.4.2-intel-2015b, 1.4.2-intel-2016a, 1.5.0-foss-2016a, 1.5.0-foss-2016b, 1.5.0-intel-2015b, 1.5.0-intel-2016a, 1.5.1-intel-2017a, 1.5.2-GCCcore-6.3.0, 1.5.2-GCCcore-6.4.0, 1.5.0-intel-2017a, 1.5.0-intel-2016b, 1.5.3-GCCcore-6.4.0, 1.5.1-foss-2016b, 1.5.3-GCCcore-5.4.0

Command: module load libjpeg-turbo

[edit] libpciaccess

Available versions: 0.13.4-foss-2016b, 0.13.4-goolf-1.7.20, 0.13.4-intel-2016a

Command: module load libpciaccess

[edit] libpthread-stubs

Available versions: 0.3-foss-2015b, 0.3-foss-2016a, 0.3-foss-2016b, 0.3-goolf-1.7.20, 0.3-intel-2015b, 0.3-intel-2016a

Command: module load libpthread-stubs

[edit] libsodium

Available versions: 1.0.8-foss-2016a

Command: module load libsodium

[edit] libtasn1

Available versions: 4.7-GNU-4.9.3-2.25

Command: module load libtasn1

[edit] libtool

Homepage: http://www.gnu.org/software/libtool

Description: GNU libtool is a generic library support script. Libtool hides the complexity of using shared librariesbehind a consistent, portable interface.

Available versions: 2.4.2-foss-2016a, 2.4.2-intel-2016a, 2.4.5-GCC-4.8.4, 2.4.6, 2.4.6-GCC-4.8.4, 2.4.6-GCC-4.9.3-2.25, 2.4.6-GNU-4.9.3-2.25, 2.4.6-foss-2016a, 2.4.6-foss-2016b, 2.4.6-goolf-1.7.20, 2.4.6-intel-2015b, 2.4.6-intel-2016a, 2.4.6-GCCcore-6.3.0, 2.4.6-GCC-5.4.0-2.26, 2.4.6-intel-2017a, 2.4.6-GCCcore-6.4.0, 2.4.6-GCCcore-7.3.0, 2.4.6-GCCcore-5.4.0

Command: module load libtool

[edit] libunistring

Available versions: 0.9.3-GNU-4.9.3-2.25

Command: module load libunistring

[edit] libxcb

Available versions: 1.11-goolf-1.7.20-Python-2.7.9, 1.11.1-foss-2016a, 1.11.1-foss-2016b, 1.11.1-goolf-1.7.20, 1.11.1-intel-2015b, 1.11.1-intel-2015b-Python-2.7.10, 1.11.1-intel-2016a, 1.8-foss-2016a-Python-2.7.3

Command: module load libxcb

[edit] libxkbcommon

Available versions: 0.6.1-intel-2016a

Command: module load libxkbcommon

[edit] libxslt

Homepage: http://xmlsoft.org/

Description: Libxslt is the XSLT C library developed for the GNOME project(but usable outside of the Gnome platform).

Available versions: 1.1.28-intel-2016a, 1.1.28-foss-2016a, 1.1.29-intel-2016a, 1.1.32-intel-2016a, 1.1.29-intel-2017a

Command: module load libxslt

[edit] libsndfile

Homepage: http://www.mega-nerd.com/libsndfile

Description: Libsndfile is a C library for reading and writing files containing sampled sound(such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.

Available versions: 1.0.28-intel-2017a, 1.0.28-GCCcore-6.4.0

Command: module load libsndfile

[edit] libyaml

Homepage: http://pyyaml.org/wiki/LibYAML

Description: LibYAML is a YAML 1.1 parser and emitter written in C.

Available versions: 0.1.6-intel-2016a, 0.1.6-intel-2017a, 0.1.7-intel-2016a

Command: module load libyaml

[edit] libspatialindex

Homepage: http://libspatialindex.github.io

Description: C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API

Available versions: 1.8.5-foss-2016b, 1.8.5-intel-2016a

Command: module load libspatialindex

[edit] libspatialite

Homepage: https://www.gaia-gis.it/fossil/libspatialite/home

Description: SpatiaLite is an open source library intended to extend the SQLite core to supportfully fledged Spatial SQL capabilities.

Available versions: 4.3.0a-foss-2016b, 4.3.0a-intel-2016a

Command: module load libspatialite

[edit] LoFreq

Homepage: http://csb5.github.io/lofreq

Description: Fast and sensitive variant calling from next-gen sequencing data

Available versions: 2.1.2-intel-2017a-Python-2.7.12

Command: module load LoFreq

[edit] LibUUID

Homepage: http://sourceforge.net/projects/libuuid/

Description: Portable uuid C library

Available versions: 1.0.3-foss-2016a

Command: module load LibUUID

[edit] LAME

Homepage: http://lame.sourceforge.net/

Description: LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.

Available versions: 3.99.5-foss-2016b

Command: module load LAME

[edit] LZO

Homepage: http://www.oberhumer.com/opensource/lzo/

Description: Portable lossless data compression library

Available versions: 2.10-foss-2016b

Command: module load LZO

[edit] libgeotiff

Homepage: https://directory.fsf.org/wiki/Libgeotiff

Description: Library for reading and writing coordinate system information from/to GeoTIFF files

Available versions: 1.4.2-foss-2018a

Command: module load libgeotiff

[edit] lua

Available versions: 5.3.4

Command: module load lua

[edit] lapack

Available versions: gcc/64/3.8.0

Command: module load lapack

[edit] MEGA2

Available versions: 4.9.1

Command: module load rc/MEGA2

[edit] Mathematica

Available versions: 10.3

Command: module load rc/Mathematica

[edit] manta

Available versions: 1.0.3

Command: module load rc/manta

[edit] mat

Available versions: test

Command: module load rc/mat

[edit] matlab

Available versions: R2012a, R2013a, R2015a, R2015b, R2016a, R2016b, R2017a, R2018a, R2017b, R2019a

Command: module load rc/matlab

[edit] metasv

Available versions: 0.5.2

Command: module load rc/metasv

[edit] mriconvert

Available versions: 2.0.8

Command: module load rc/mriconvert

[edit] maskface

Available versions: 12272017

Command: module load rc/maskface

[edit] M4

Homepage: http://www.gnu.org/software/m4/m4.html

Description: GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatiblealthough it has some extensions (for example, handling more than 9 positional parameters to macros).GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.

Available versions: 1.4.16-foss-2016a, 1.4.17, 1.4.17-GCC-4.8.4, 1.4.17-GCC-4.9.3-2.25, 1.4.17-GCC-4.9.3-binutils-2.25, 1.4.17-GCCcore-4.9.3, 1.4.17-GCCcore-5.4.0, 1.4.17-GNU-4.9.3-2.25, 1.4.17-foss-2016a, 1.4.17-foss-2016b, 1.4.17-goolf-1.7.20, 1.4.17-intel-2015b, 1.4.17-intel-2016a, 1.4.18-GCCcore-6.3.0, 1.4.17-GCCcore-6.1.0, 1.4.17-GCC-5.4.0-2.26, 1.4.17-intel-2017a, 1.4.16, 1.4.18, 1.4.18-GCCcore-6.4.0, 1.4.18-GCCcore-7.3.0, 1.4.18-GCCcore-5.4.0

Command: module load M4

[edit] MACH

Available versions: 1.0.18

Command: module load MACH

[edit] MACS

Available versions: 1.4.2-1-goolf-1.7.20-Python-2.7.5

Command: module load MACS

[edit] MOSAIK

Homepage: https://code.google.com/p/mosaik-aligner/

Description: MOSAIK is a reference-guided aligner for next-generationsequencing technologies

Available versions: 2.2.28-intel-2016a-20140425-24cf06

Command: module load MOSAIK

[edit] MPICH

Available versions: 3.0.4-GCC-4.8.1

Command: module load MPICH

[edit] MRIcroGL

Available versions: 09302016

Command: module load MRIcroGL

[edit] MRIcron

Available versions: 06_22_15

Command: module load MRIcron

[edit] MRtrix

Available versions: 0.3.14-intel-2016a-Python-2.7.11, 0.3.16-intel-2016a-Python-2.7.11

Command: module load MRtrix

[edit] MUSCLE

Homepage: http://drive5.com/muscle/

Description: MUSCLE is one of the best-performing multiple alignment programsaccording to published benchmark tests, with accuracy and speed that are consistentlybetter than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most userslearn everything they need to know about MUSCLE in a few minutes—only a handful ofcommand-line options are needed to perform common alignment tasks.

Available versions: 3.8.31-intel-2016a

Command: module load MUSCLE

[edit] MVAPICH2

Available versions: 2.2b-GCC-4.9.3-2.25

Command: module load MVAPICH2

[edit] Maq

Available versions: 0.7.0

Command: module load Maq

[edit] Mathematica

Available versions: 11.0.1

Command: module load Mathematica

[edit] Maven

Homepage: http://maven.apache.org/index.html}

Available versions: 3.3.9

Command: module load Maven

[edit] Mercurial

Homepage: http://mercurial.selenic.com/

Description: Mercurial is a free, distributed source control management tool. It efficiently handles projectsof any size and offers an easy and intuitive interface.

Available versions: 2.5.2-goolf-1.7.20-Python-2.7.3, 3.8.3-foss-2016a-Python-2.7.11, 3.8.3-intel-2016a-Python-2.7.11, 3.2.4-foss-2015b-Python-2.7.9

Command: module load Mercurial

[edit] Mesa

Homepage: http://www.mesa3d.org/

Description: Mesa is an open-source implementation of the OpenGL specification -a system for rendering interactive 3D graphics.

Available versions: 11.1.2-intel-2016a, 11.2.1-intel-2016a, 12.0.2-foss-2016b, 17.0.2-intel-2017a, 17.3.6-foss-2018a, 11.1.2-foss-2016b

Command: module load Mesa

[edit] Minimac2

Available versions: 2014.9.15-intel-2015b

Command: module load Minimac2

[edit] Minimac3

Available versions: 1.0.10-intel-2015b

Command: module load Minimac3

[edit] makedepend

Homepage: http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html

Description: The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.

Available versions: 1.0.5-intel-2016a, 1.0.5-foss-2016b

Command: module load makedepend

[edit] matplotlib

Homepage: http://matplotlib.org

Description: matplotlib is a python 2D plotting library which produces publication quality figures in a variety ofhardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the pythonand ipython shell, web application servers, and six graphical user interface toolkits.

Available versions: 1.3.1-intel-2015b-Python-2.7.8, 1.5.1-intel-2016a-Python-2.7.11, 1.5.3-foss-2016b-Python-2.7.12, 2.0.0-foss-2016b-Python-2.7.12, 2.0.2-foss-2016b-Python-2.7.12, 2.0.2-intel-2017a-Python-2.7.13-libpng-1.6.29, 1.5.1-foss-2016a-Python-2.7.11

Command: module load matplotlib

[edit] motif

Available versions: 2.3.5-foss-2016a, 2.3.5-intel-2016a, 2.3.7-intel-2016a

Command: module load motif

[edit] MACS2

Homepage: https://github.com/taoliu/MACS/

Description: Model Based Analysis for ChIP-Seq data

Available versions: 2.1.0.20150731-foss-2016a-Python-2.7.11, 2.1.1.20160309-foss-2016a-Python-2.7.11

Command: module load MACS2

[edit] MEME

Homepage: http://meme-suite.org/

Description: The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) orGLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs usingMAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associatemotifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichmentusing SpaMo or CentriMo.

Available versions: 4.12.0-foss-2016a

Command: module load MEME

[edit] MultiQC

Available versions: 0.9-foss-2016b-Python-2.7.12, 1.2-foss-2016b-Python-2.7.12, 1.4-foss-2016b-Python-2.7.12, 0.8, 0.8~

Command: module load MultiQC

[edit] Mono

Homepage: http://www.mono-project.com/

Description: An open source, cross-platform, implementation of C# and the CLR that isbinary compatible with Microsoft.NET.

Available versions: 4.8.0.495-intel-2017a, 5.2.0.224-intel-2017a

Command: module load Mono

[edit] MaSuRCA

Homepage: http://www.genome.umd.edu/masurca.html

Description: MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graphand Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containingonly short reads from Illumina sequencing or a mixture of short reads and long reads(Sanger, 454, Pacbio and Nanopore).

Available versions: 3.2.4-foss-2018a, 3.2.6-foss-2018a

Command: module load MaSuRCA

[edit] minimap2

Homepage: https://github.com/lh3/minimap2

Description: Minimap2 is a fast sequence mapping and alignment program that can find overlaps betweenlong noisy reads, or map long reads or their assemblies to a reference genome optionally with detailedalignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limitedtest data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replaceBWA-MEM for long reads and contig alignment.

Available versions: 2.0rc1-foss-2016b

Command: module load minimap2

[edit] MotionCor2

Homepage: http://msg.ucsf.edu/em/software/motioncor2.html

Description: MotionCor2 is a multi-GPU program that corrects beam-induced sample motion recordedon dose fractionated movie stacks

Available versions: 1.0.4, 1.0.5

Command: module load MotionCor2

[edit] mpich

Available versions: ge/gcc/64/3.2.1

Command: module load mpich

[edit] mpiexec

Available versions: 0.84_432

Command: module load mpiexec

[edit] mvapich2

Available versions: gcc/64/2.3b

Command: module load mvapich2

[edit] NAMD

Available versions: 2.12b1-gpu, 2.12, 2.13b2-gpu

Command: module load rc/NAMD

[edit] nccl

Homepage: https://developer.nvidia.com/nccl

Description: The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collectivecommunication primitives that are performance optimized for NVIDIA GPUs.

Available versions: 1.3.4-1

Command: module load rc/nccl

[edit] ncdu

Available versions: 1.13-20.1

Command: module load rc/ncdu

[edit] nighres

Available versions: 1.1.0b1

Command: module load rc/nighres

[edit] NASM

Homepage: http://www.nasm.us/

Description: NASM: General-purpose x86 assembler

Available versions: 2.07-intel-2015b, 2.07-intel-2016a, 2.11.06-goolf-1.7.20, 2.11.08-foss-2015b, 2.11.08-foss-2016a, 2.11.08-foss-2016b, 2.11.08-intel-2015b, 2.11.08-intel-2016a, 2.12.02-foss-2016a, 2.12.02-foss-2016b, 2.12.02-intel-2015b, 2.12.02-intel-2016a, 2.12.02-intel-2017a, 2.13.01-GCCcore-6.3.0, 2.13.01-GCCcore-6.4.0, 2.12.02-intel-2016b, 2.13.03-GCCcore-6.4.0, 2.13.03-GCCcore-5.4.0

Command: module load NASM

[edit] NGS

Available versions: 1.2.5-foss-2016b

Command: module load NGS

[edit] ncbi-vdb

Available versions: 2.7.0-foss-2016b

Command: module load ncbi-vdb

[edit] netCDF

Homepage: http://www.unidata.ucar.edu/software/netcdf/

Description: NetCDF (network Common Data Form) is a set of software librariesand machine-independent data formats that support the creation, access, and sharing of array-orientedscientific data.

Available versions: 4.3.3.1-foss-2016a, 4.3.3.1-intel-2016a, 4.4.0-intel-2016a, 4.4.1-foss-2016a, 4.4.1-foss-2016b, 4.4.1-intel-2015b, 4.4.1-intel-2016a, 4.4.1.1-intel-2017a, 4.4.1.1-foss-2016b, 4.4.1.1-intel-2016a, 4.6.0-foss-2018a

Command: module load netCDF

[edit] nodejs

Available versions: 4.4.7-foss-2016a

Command: module load nodejs

[edit] numactl

Homepage: http://oss.sgi.com/projects/libnuma/

Description: The numactl program allows you to run your application program on specificcpu's and memory nodes. It does this by supplying a NUMA memory policy tothe operating system before running your program. The libnuma library providesconvenient ways for you to add NUMA memory policies into your own program.

Available versions: 2.0.10-GCC-4.8.4, 2.0.10-GNU-4.9.3-2.25, 2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25, 2.0.11-GCC-4.9.3-2.25, 2.0.11-GCC-5.4.0-2.26, 2.0.11-GCCcore-6.3.0, 2.0.11-intel-2017a, 2.0.11-GCC-6.1.0-2.27, 2.0.11-GCC-6.3.0-2.27, 2.0.11-GCCcore-6.4.0, 2.0.11-intel-2016a, 2.0.11-GCCcore-7.3.0

Command: module load numactl

[edit] numpy

Homepage: http://www.numpy.org

Description: NumPy is the fundamental package for scientific computing with Python. It contains among other things:a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortrancode, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses,NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can bedefined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.

Available versions: 1.10.4-intel-2016a-Python-2.7.11, 1.8.2-intel-2015b-Python-2.7.11, 1.8.2-foss-2016a-Python-2.7.11, 1.10.1-goolf-1.7.20-Python-2.7.11

Command: module load numpy

[edit] NLopt

Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt

Description: NLopt is a free/open-source library for nonlinear optimization,providing a common interface for a number of different free optimization routinesavailable online as well as original implementations of various other algorithms.

Available versions: 2.4.2-intel-2017a, 2.4.2-foss-2016b, 2.4.2-foss-2018a

Command: module load NLopt

[edit] NiBabel

Homepage: https://nipy.github.io/nibabel

Description: NiBabel provides read/write access to some common medical and neuroimaging file formats,including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECATas well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry andannotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.

Available versions: 2.1.0-intel-2017a-Python-2.7.13

Command: module load NiBabel

[edit] ngmlr

Homepage: https://github.com/philres/ngmlr

Description: Ngmlr is a long-read mapper designed to align PacBilo or Oxford Nanopore to areference genome with a focus on reads that span structural variations.

Available versions: 0.2.6-foss-2016b

Command: module load ngmlr

[edit] NCBI-Toolkit

Homepage: http://ncbi.github.io/cxx-toolkit/

Description: The NCBI Toolkit is a collection of utilities developed for theproduction and distribution of GenBank, Entrez, BLAST, and related servicesby the National Center for Biotechnology Information.

Available versions: 18.0.0-intel-2017a

Command: module load NCBI-Toolkit

[edit] NCCL

Homepage: https://developer.nvidia.com/nccl

Description: The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collectivecommunication primitives that are performance optimized for NVIDIA GPUs.

Available versions: 2.2.13-CUDA-9.2.148.1, 2.2.13-CUDA-8.0.61

Command: module load NCCL

[edit] netcdf

Available versions: gcc/64/4.5.0

Command: module load netcdf

[edit] netperf

Available versions: 2.7.0

Command: module load netperf

[edit] openscenegraph

Available versions: 3.2.1

Command: module load rc/openscenegraph

[edit] OTF

Available versions: 1.12.4-gompi-1.5.12

Command: module load OTF

[edit] OpenPGM

Available versions: 5.2.122-foss-2016a, 5.2.122-intel-2015b

Command: module load OpenPGM

[edit] OpenSSL

Homepage: http://www.openssl.org/

Description: The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured,and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1)protocols as well as a full-strength general purpose cryptography library.

Available versions: 1.0.2g-GCCcore-4.9.3, 1.0.2h-foss-2016b

Command: module load OpenSSL

[edit] OpenMM

Homepage: https://simtk.org/home/openmm

Description: OpenMM is a toolkit for molecular simulation.

Available versions: 6.3-intel-2016a-Python-2.7.11

Command: module load OpenMM

[edit] openmpi

Available versions: mlnx/gcc/64/3.1.1rc1, gcc/64/1.10.7

Command: module load openmpi

[edit] openblas

Available versions: .version, dynamic/0.2.20

Command: module load openblas

[edit] parsync

Available versions: 1.69

Command: module load rc/parsync

[edit] PCRE

Homepage: http://www.pcre.org/

Description: The PCRE library is a set of functions that implement regular expressionpattern matching using the same syntax and semantics as Perl 5.

Available versions: 8.38-foss-2016a, 8.38-foss-2016b, 8.38-intel-2015b, 8.38-intel-2016a, 8.39-intel-2015b, 8.39-intel-2016a, 8.39-foss-2016b, 8.40-intel-2017a, 8.41-GCCcore-6.3.0, 8.12-goolf-1.4.10, 8.12-intel-2016a, 8.41-GCCcore-6.4.0, 8.39-intel-2016b, 8.40-foss-2016b, 8.41-GCCcore-5.4.0

Command: module load PCRE

[edit] PDT

Available versions: 3.20-goolf-1.7.20

Command: module load PDT

[edit] PETSc

Available versions: 3.6.3-intel-2015b-Python-2.7.11

Command: module load PETSc

[edit] PGI

Homepage: http://www.pgroup.com/

Description: C, C++ and Fortran compilers from The Portland Group - PGI

Available versions: 17.10-GCC-6.3.0-2.27, 17.4-GCC-6.3.0-2.27, 18.5-GCC-6.4.0-2.28

Command: module load PGI

[edit] PHASE

Available versions: 2.1.1

Command: module load PHASE

[edit] PIL

Available versions: 1.1.7-intel-2015b-Python-2.7.11, 1.1.7-intel-2016a-Python-2.7.11

Command: module load PIL

[edit] PROJ

Homepage: http://trac.osgeo.org/proj/

Description: Program proj is a standard Unix filter function which convertsgeographic longitude and latitude coordinates into cartesian coordinates

Available versions: 4.9.2-foss-2016a, 4.9.2-foss-2016b, 4.9.2-intel-2015b, 4.9.2-intel-2016a, 4.9.3-intel-2017a, 4.9.3-foss-2016b, 4.9.3-intel-2016a, 5.0.0-foss-2018a

Command: module load PROJ

[edit] Pango

Homepage: http://www.pango.org/

Description: Pango is a library for laying out and rendering of text, with an emphasis on internationalization.Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in thecontext of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.

Available versions: 1.39.0-foss-2016b, 1.39.0-intel-2016a, 1.40.1-intel-2016a, 1.40.12-intel-2017a

Command: module load Pango

[edit] Pindel

Homepage: http://gmt.genome.wustl.edu/packages/pindel/

Description: Pindel can detect breakpoints of large deletions, medium sizedinsertions, inversions, tandem duplications and other structural variants at single-basedresolution from next-gen sequence data. It uses a pattern growth approach to identify thebreakpoints of these variants from paired-end short reads.

Available versions: 0.2.5b8-foss-2016b

Command: module load Pindel

[edit] ProbABEL

Available versions: 0.5.0

Command: module load ProbABEL

[edit] PyCairo

Available versions: 1.10.0-intel-2016a-Python-2.7.11

Command: module load PyCairo

[edit] PyGObject

Available versions: 2.28.6-intel-2016a-Python-2.7.11

Command: module load PyGObject

[edit] PyGTK

Available versions: 2.24.0-intel-2016a-Python-2.7.11

Command: module load PyGTK

[edit] PyQt

Available versions: 4.11.3-goolf-1.7.20-Python-2.7.9, 4.11.4-foss-2016a-Python-2.7.11, 4.11.4-intel-2016a-Python-2.7.11

Command: module load PyQt

[edit] PyZMQ

Available versions: 14.7.0-intel-2015b-Python-2.7.9-zmq3, 15.3.0-foss-2016a-Python-3.5.1-zmq4

Command: module load PyZMQ

[edit] Pygments

Available versions: 2.0.2-intel-2015b-Python-2.7.9

Command: module load Pygments

[edit] Pysam

Available versions: 0.9.1.4-foss-2016a-Python-2.7.12, 0.9.1.4-foss-2016b-Python-2.7.12

Command: module load Pysam

[edit] p11-kit

Available versions: 0.23.2-GNU-4.9.3-2.25

Command: module load p11-kit

[edit] parallel

Available versions: 20150822-GCC-4.9.2

Command: module load parallel

[edit] path.py

Available versions: 8.2.1-foss-2016a-Python-3.5.1

Command: module load path.py

[edit] perl-app-cpanminus

Available versions: 1.7039

Command: module load perl-app-cpanminus

[edit] pixman

Homepage: http://www.pixman.org/

Description: Pixman is a low-level software library for pixel manipulation, providingfeatures such as image compositing and trapezoid rasterization. Importantusers of pixman are the cairo graphics library and the X server.

Available versions: 0.34.0-foss-2016b, 0.34.0-intel-2015b, 0.34.0-intel-2016a, 0.34.0-GCCcore-6.3.0, 0.34.0-GCCcore-6.4.0, 0.34.0-foss-2016a, 0.34.0-intel-2016b, 0.32.6-intel-2016a, 0.34.0-GCCcore-5.4.0

Command: module load pixman

[edit] pkgconfig

Available versions: 1.1.0-intel-2016a-Python-2.7.11

Command: module load pkgconfig

[edit] printproto

Available versions: 1.0.5-foss-2015b, 1.0.5-foss-2016a, 1.0.5-goolf-1.7.20, 1.0.5-intel-2016a

Command: module load printproto

[edit] prompt-toolkit

Available versions: 1.0.3-foss-2016a-Python-3.5.1

Command: module load prompt-toolkit

[edit] pysqlite

Available versions: 2.6.3-intel-2015b-Python-2.7.9

Command: module load pysqlite

[edit] protobuf

Homepage: https://github.com/google/protobuf/

Description: Google Protocol Buffers

Available versions: 3.3.0-intel-2017a

Command: module load protobuf

[edit] protobuf-python

Homepage: https://github.com/google/protobuf/

Description: Python Protocol Buffers runtime library.

Available versions: 3.3.0-intel-2017a-Python-3.6.1

Command: module load protobuf-python

[edit] PyYAML

Homepage: https://pypi.python.org/pypi/PyYAML/

Description: PyYAML is a YAML parser and emitter for the Python programming language.

Available versions: 3.12-intel-2016a-Python-3.5.1

Command: module load PyYAML

[edit] prodigal

Homepage: http://prodigal.ornl.gov/

Description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)is a microbial (bacterial and archaeal) gene finding program developedat Oak Ridge National Laboratory and the University of Tennessee.

Available versions: 2.6.2-GCC-4.9.3-binutils-2.25

Command: module load prodigal

[edit] Pillow

Homepage: http://pillow.readthedocs.org/

Description: Pillow is the 'friendly PIL fork' by Alex Clark and Contributors.PIL is the Python Imaging Library by Fredrik Lundh and Contributors.

Available versions: 4.3.0-intel-2017a-Python-2.7.13

Command: module load Pillow

[edit] p7zip

Homepage: http://p7zip.sourceforge.net/

Description: p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix.7-Zip is a file archiver with highest compression ratio.

Available versions: 9.38.1

Command: module load p7zip

[edit] patchelf

Homepage: http://nixos.org/patchelf.html

Description: PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.

Available versions: 0.9-intel-2016a, 0.9-foss-2016b

Command: module load patchelf

[edit] PCRE2

Homepage: http://www.pcre.org/

Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntaxand semantics as Perl 5.

Available versions: 10.21-foss-2016b, 10.31-foss-2018a

Command: module load PCRE2

[edit] qdirstat

Available versions: 1.4

Command: module load rc/qdirstat

[edit] Qt

Available versions: 4.8.6-goolf-1.7.20, 4.8.7-foss-2016a, 4.8.7-foss-2016b, 4.8.7-intel-2016a

Command: module load Qt

[edit] Qwt

Homepage: http://qwt.sourceforge.net/

Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programswith a technical background.

Available versions: 6.1.3-foss-2016b, 6.1.3-intel-2016a

Command: module load Qwt

[edit] QwtPolar

Homepage: http://qwtpolar.sourceforge.net/

Description: The QwtPolar library contains classes for displaying values on a polar coordinate system.

Available versions: 1.1.1-foss-2016b, 1.1.1-intel-2016a

Command: module load QwtPolar

[edit] QUAST

Homepage: http://quast.sourceforge.net/quast

Description: QUAST evaluates genome assemblies.

Available versions: 4.4-foss-2016a-Python-2.7.11, 4.6.3-foss-2016a-Python-2.7.11

Command: module load QUAST

[edit] QIIME

Available versions: qiime-dependencies

Command: module load QIIME

[edit] QWRAP

Available versions: v3

Command: module load QWRAP

[edit] RStudio

Available versions: 1.0.136, 1.0.44

Command: module load rc/RStudio

[edit] relion

Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page

Description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computerprogram that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D classaverages in electron cryo-microscopy (cryo-EM).

Available versions: 1.4, 2.0_beta, 2.1

Command: module load rc/relion

[edit] rserver

Available versions: 3.4.3, 3.5.2, 3.5.2_X11

Command: module load rc/rserver

[edit] R

Available versions: 2.15.3-goolf-1.7.20, 3.0.1-goolf-1.4.10-bare, 3.2.0-goolf-1.7.20, 3.2.1-goolf-1.7.20, 3.2.3-foss-2016a-bare, 3.2.3-intel-2016a-bare, 3.3.1-foss-2016b, 3.3.1-foss-2016b-no-X, 3.3.1-intel-2016a-bare, 3.4.1-intel-2017a-X11-20170314, 3.3.3-intel-2017a-X11-20170314, 3.4.3-intel-2017a-X11-20170314, .3.4.3-foss-2016b-X11-20160819.bak_20180502163551, 3.4.3-foss-2016b-X11-20160819, 3.5.0-intel-2017a-X11-20170314-bare, 3.5.0-foss-2018a-X11-20180131-bare, 3.5.1-foss-2018a-X11-20180131-bare, DESeq2.R-3.3.1-foss-2016b-no-X, DESeq2.R-3.4.3-intel-2017a-X11-20170314

Command: module load R

[edit] RAxML

Available versions: 8.1.1-goolf-1.4.10-mt-avx

Command: module load RAxML

[edit] RSeQC

Available versions: 2.6.3-goolf-1.7.20-Python-2.7.10-R-3.2.1

Command: module load RSeQC

[edit] Ruby

Available versions: 2.3.3

Command: module load Ruby

[edit] randrproto

Available versions: 1.5.0-goolf-1.7.20, 1.5.0-intel-2015b, 1.5.0-intel-2016a

Command: module load randrproto

[edit] renderproto

Available versions: 0.11-foss-2016a, 0.11-foss-2016b, 0.11-goolf-1.7.20, 0.11-intel-2015b, 0.11-intel-2016a

Command: module load renderproto

[edit] requests

Available versions: 2.7.0-intel-2015b-Python-2.7.9

Command: module load requests

[edit] ResMap

Homepage: http://resmap.sourceforge.net/

Description: ResMap (Resolution Map) is a Python (NumPy/SciPy) application with a Tkinter GUI.It is an easy to use software package for computing the local resolution of 3D density mapsstudied in structural biology, primarily electron cryo-microscopy (cryo-EM).

Available versions: 1.1.4

Command: module load ResMap

[edit] RELION

Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page

Description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computerprogram that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D classaverages in electron cryo-microscopy (cryo-EM).

Available versions: 2.1-intel-2016a-CUDA-8.0.44

Command: module load RELION

[edit] Rust

Homepage: https://www.rust-lang.org

Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults,and guarantees thread safety.

Available versions: 1.30.1-foss-2016b

Command: module load Rust

[edit] snakemakeslurm_local

Available versions: 4.8.0-1

Command: module load snakemakeslurm_local

[edit] SAS

Available versions: v9.4

Command: module load rc/SAS

[edit] Salmon

Available versions: 0.7.2

Command: module load rc/Salmon

[edit] soapsv

Available versions: 1.3

Command: module load rc/soapsv

[edit] snakemake

Available versions: 4.0.0, 4.8.0

Command: module load rc/snakemake

[edit] sublime_text

Available versions: 3

Command: module load rc/sublime_text

[edit] S.A.G.E.

Available versions: 6.3

Command: module load S.A.G.E.

[edit] SCOTCH

Available versions: 6.0.4-intel-2015b

Command: module load SCOTCH

[edit] SHRiMP

Available versions: 2.2.3-goolf-1.4.10

Command: module load SHRiMP

[edit] SIP

Available versions: 4.16.4-goolf-1.7.20-Python-2.7.9, 4.16.4-intel-2015b-Python-2.7.9, 4.16.8-intel-2015b-Python-2.7.9, 4.18-foss-2016a-Python-2.7.11, 4.18-intel-2016a-Python-2.7.11

Command: module load SIP

[edit] SOLAR-Eclipse

Available versions: 8.1.1

Command: module load SOLAR-Eclipse

[edit] SPAdes

Homepage: http://cab.spbu.ru/software/spades/

Description: Genome assembler for single-cell and isolates data sets

Available versions: 3.9.0-foss-2016a, 3.12.0-foss-2016b

Command: module load SPAdes

[edit] SPPARKS

Available versions: 07192016-intel-2016a

Command: module load SPPARKS

[edit] STAR-Fusion

Available versions: 0.8.0-goolf-1.4.10-Perl-5.16.3

Command: module load STAR-Fusion

[edit] STAR

Available versions: 2.5.1b-goolf-1.4.10, 2.5.2a-foss-2016a, 2.5.4b-intel-2017a, 2.5.4b-foss-2016b, 2.5.2b, 2.5.2b~

Command: module load STAR

[edit] SWIG

Homepage: http://www.swig.org/

Description: SWIG is a software development tool that connects programs written in C and C++ witha variety of high-level programming languages.

Available versions: 3.0.10-intel-2016a-Python-2.7.12-PCRE-8.39, 3.0.12-intel-2017a-Python-2.7.13, 3.0.11-foss-2016b-Python-2.7.12, 3.0.11-intel-2016a-Python-2.7.12, 3.0.8-intel-2016a-Python-2.7.11, 3.0.12-foss-2018a-Python-3.6.4, 3.0.12-foss-2018a-Python-2.7.14

Command: module load SWIG

[edit] ScientificPython

Available versions: 2.9.4-intel-2015b-Python-2.7.11

Command: module load ScientificPython

[edit] Spack

Available versions: 0.10.0

Command: module load Spack

[edit] scipy

Available versions: 0.17.0-intel-2016a-Python-2.7.11

Command: module load scipy

[edit] shapeit

Available versions: 2.r837.GLIBCv2.12_linux_x86_64

Command: module load shapeit

[edit] sympy

Available versions: 0.7.6.1-intel-2015b-Python-2.7.11

Command: module load sympy

[edit] SRA-Toolkit

Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std

Description: The NCBI SRA Toolkit enables reading (dumping) of sequencing filesfrom the SRA database and writing (loading) files into the .sra format

Available versions: 2.5.4-1-centos_linux64, 2.8.2-1-centos_linux64

Command: module load SRA-Toolkit

[edit] sparsehash

Homepage: https://code.google.com/p/sparsehash/

Description: An extremely memory-efficient hash_mapimplementation. 2 bits/entry overhead! The SparseHash librarycontains several hash-map implementations, includingimplementations that optimize for space or speed.

Available versions: 2.0.2-foss-2016a

Command: module load sparsehash

[edit] Spark

Homepage: http://spark.apache.org

Description: Spark is Hadoop MapReduce done in memory

Available versions: 2.2.0-Hadoop-2.6-Java-1.8.0_144

Command: module load Spark

[edit] summovie

Homepage: http://grigoriefflab.janelia.org/unblur

Description: Movie frame sums can be calculated using summovie,which uses the alignment results from a prior run of Unblur.

Available versions: 1.0.2

Command: module load summovie

[edit] snakemakeslurm

Available versions: 4.8.0, 4.8.0-2, 4.8.0-1

Command: module load snakemakeslurm

[edit] scalapack

Available versions: openmpi/gcc/64/2.0.2

Command: module load scalapack

[edit] sge

Available versions: 2011.11p1

Command: module load sge

[edit] slurm

Available versions: 17.11.8

Command: module load slurm

[edit] tortoise

Available versions: 2.5.2b, 3.0.0, 3.1.2

Command: module load rc/tortoise

[edit] transdecoder

Available versions: 5.3.0

Command: module load rc/transdecoder

[edit] torch

Available versions: 7

Command: module load rc/torch

[edit] tarquin

Available versions: 4.3.10

Command: module load rc/tarquin

[edit] tcllib

Available versions: 1.19

Command: module load rc/tcllib

[edit] Tar

Available versions: 1.29-goolf-1.4.10

Command: module load Tar

[edit] Tk

Homepage: http://www.tcl.tk/

Description: Tk is an open source, cross-platform widget toolchain that provides a library of basic elements forbuilding a graphical user interface (GUI) in many different programming languages.

Available versions: 8.6.3-foss-2015b-no-X11, 8.6.3-goolf-1.7.20-no-X11, 8.6.3-intel-2015b-no-X11, 8.6.4-foss-2015b-no-X11, 8.6.4-foss-2016a-no-X11, 8.6.4-foss-2016b-no-X11, 8.6.4-goolf-1.7.20, 8.6.4-goolf-1.7.20-no-X11, 8.6.4-intel-2015b-no-X11, 8.6.4-intel-2016a-no-X11, 8.6.5-foss-2016a, 8.6.5-foss-2016b, 8.6.5-intel-2015b, 8.6.5-intel-2016a, 8.6.6-intel-2017a, 8.6.5-intel-2017a, 8.6.8-foss-2018a

Command: module load Tk

[edit] TopHat

Available versions: 2.1.0-intel-2015b, 2.1.1-foss-2016a

Command: module load TopHat

[edit] Trim_Galore

Available versions: 0.4.2-foss-2016b, 0.4.4-foss-2016b

Command: module load Trim_Galore

[edit] Trimmomatic

Available versions: 0.36-Java-1.8.0_92

Command: module load Trimmomatic

[edit] Trinity

Available versions: 2.2.0-foss-2016a

Command: module load Trinity

[edit] tabix

Available versions: 0.2.6-goolf-1.7.20, 0.2.6-intel-2015b

Command: module load tabix

[edit] tcsh

Available versions: 6.18.01-goolf-1.7.20, 6.18.01-intel-2015b, 6.19.00-foss-2015b, 6.19.00-foss-2016a, 6.19.00-foss-2016b, 6.19.00-intel-2016a

Command: module load tcsh

[edit] testpath

Available versions: 0.3-foss-2016a-Python-3.5.1

Command: module load testpath

[edit] texinfo

Homepage: https://www.gnu.org/software/texinfo/

Description: Texinfo is the official documentation format of the GNU project.

Available versions: 4.13a, 6.4-GCCcore-5.4.0

Command: module load texinfo

[edit] Tensorflow

Homepage: https://www.tensorflow.org/

Description: An open-source software library for Machine Intelligence

Available versions: 1.2.0-intel-2017a-Python-3.6.1

Command: module load Tensorflow

[edit] TransDecoder

Homepage: https://github.com/TransDecoder/TransDecoder/wiki

Description: TransDecoder identifies candidate coding regions within transcript sequences,such as those generated by de novo RNA-Seq transcript assembly using Trinity,or constructed based on RNA-Seq alignments to the genome usingTophat and Cufflinks.

Available versions: 5.1.0-intel-2017a-Perl-5.24.1

Command: module load TransDecoder

[edit] trim_galore

Available versions: 0.4.2, 0.4.2~

Command: module load trim_galore

[edit] torque

Available versions: 6.1.1

Command: module load torque

[edit] unblur

Homepage: http://grigoriefflab.janelia.org/unblur

Description: Unblur is used to align the frames of movies recorded on an electron microscopeto reduce image blurring due to beam-induced motion.It reads stacks of movies that are stored in MRC/CCP4 format.

Available versions: 1.0.2

Command: module load unblur

[edit] usearch

Available versions: 7.0.1090

Command: module load usearch

[edit] vmd

Available versions: 1.9.3

Command: module load rc/vmd

[edit] VEGAS

Available versions: 0.8.27

Command: module load VEGAS

[edit] VICUNA

Available versions: 1.3

Command: module load VICUNA

[edit] VPhaser-2

Available versions: 02112013-intel-2016a

Command: module load VPhaser-2

[edit] VTK

Homepage: http://www.vtk.org

Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for3D computer graphics, image processing and visualization. VTK consists of a C++ class library and severalinterpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualizationalgorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniquessuch as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.

Available versions: 7.1.1-intel-2017a-Python-2.7.13, 6.3.0-foss-2016b-Python-2.7.12

Command: module load VTK

[edit] VCFtools

Homepage: https://vcftools.github.io

Description: The aim of VCFtools is to provideeasily accessible methods for working with complexgenetic variation data in the form of VCF files.

Available versions: 0.1.14-intel-2016a-Perl-5.22.1, 0.1.15-intel-2016a-Perl-5.22.1

Command: module load VCFtools

[edit] wcwidth

Available versions: 0.1.7-foss-2016a-Python-3.5.1

Command: module load wcwidth

[edit] wxPython

Homepage: http://www.wxpython.org

Description: wxPython is a GUI toolkit for the Python programming language.It allows Python programmers to create programs with a robust,highly functional graphical user interface, simply and easily.It is implemented as a Python extension module (native code)that wraps the popular wxWidgets cross platform GUI library,which is written in C++.

Available versions: 3.0.2.0-intel-2017a-Python-2.7.13

Command: module load wxPython

[edit] wxWidgets

Homepage: http://www.wxwidgets.org/

Description: wxWidgets is a C++ library that lets developers create applications for Windows,Mac OS X, Linux and other platforms with a single code base.It has language bindings for Python, Perl, Ruby and many other languages.

Available versions: 3.0.3-intel-2016a, 3.0.3-foss-2016b

Command: module load wxWidgets

[edit] xget

Available versions: xget-public

Command: module load rc/xget

[edit] XKeyboardConfig

Available versions: 2.17-intel-2016a

Command: module load XKeyboardConfig

[edit] xbitmaps

Available versions: 1.1.1-foss-2016a, 1.1.1-intel-2016a

Command: module load xbitmaps

[edit] xcb-proto

Available versions: 1.11, 1.11-goolf-1.7.20-Python-2.7.9, 1.11-intel-2015b-Python-2.7.10, 1.7-foss-2016a-Python-2.7.3

Command: module load xcb-proto

[edit] xcb-util-image

Available versions: 0.4.0-intel-2015b, 0.4.0-intel-2016a

Command: module load xcb-util-image

[edit] xcb-util-keysyms

Available versions: 0.4.0-intel-2015b, 0.4.0-intel-2016a

Command: module load xcb-util-keysyms

[edit] xcb-util-renderutil

Available versions: 0.3.9-intel-2015b, 0.3.9-intel-2016a

Command: module load xcb-util-renderutil

[edit] xcb-util-wm

Available versions: 0.4.1-intel-2015b, 0.4.1-intel-2016a

Command: module load xcb-util-wm

[edit] xcb-util

Available versions: 0.4.0-intel-2015b, 0.4.0-intel-2016a

Command: module load xcb-util

[edit] xextproto

Available versions: 7.2.1-foss-2016a, 7.2.1-intel-2016a, 7.3.0-foss-2015b, 7.3.0-foss-2016a, 7.3.0-foss-2016b, 7.3.0-goolf-1.7.20, 7.3.0-intel-2015b, 7.3.0-intel-2016a

Command: module load xextproto

[edit] xf86vidmodeproto

Available versions: 2.3.1-intel-2016a

Command: module load xf86vidmodeproto

[edit] xineramaproto

Homepage: http://www.freedesktop.org/wiki/Software/xlibs

Description: X protocol and ancillary headers for xinerama

Available versions: 1.2.1-intel-2016a, 1.2.1-foss-2016b

Command: module load xineramaproto

[edit] xorg-macros

Available versions: 1.19.0-foss-2016a, 1.19.0-foss-2016b, 1.19.0-goolf-1.7.20, 1.19.0-intel-2016a

Command: module load xorg-macros

[edit] xprop

Homepage: http://www.x.org/wiki/

Description: The xprop utility is for displaying window and font properties in an X server.One window or font is selected using the command line arguments or possiblyin the case of a window, by clicking on the desired window. A list ofproperties is then given, possibly with formatting information.

Available versions: 1.2.2-intel-2016a, 1.2.2-intel-2017a, 1.2.2-foss-2016b

Command: module load xprop

[edit] xproto

Available versions: 7.0.23-foss-2016a, 7.0.26-intel-2016a, 7.0.27-foss-2015b, 7.0.27-goolf-1.7.20, 7.0.28-foss-2016a, 7.0.28-foss-2016b, 7.0.28-goolf-1.7.20, 7.0.28-intel-2015b, 7.0.28-intel-2016a

Command: module load xproto

[edit] xtrans

Homepage: http://www.freedesktop.org/wiki/Software/xlibs}

Available versions: 1.2-foss-2016a, 1.3.4-intel-2016a, 1.3.5-foss-2015b, 1.3.5-foss-2016a, 1.3.5-foss-2016b, 1.3.5-goolf-1.7.20, 1.3.5-intel-2015b, 1.3.5-intel-2016a

Command: module load xtrans

[edit] Xerces-C++

Homepage: http://xerces.apache.org/xerces-c/

Description: Xerces-C++ is a validating XML parser written in a portablesubset of C++. Xerces-C++ makes it easy to give your application the ability toread and write XML data. A shared library is provided for parsing, generating,manipulating, and validating XML documents using the DOM, SAX, and SAX2APIs.

Available versions: 3.1.2-intel-2015b

Command: module load Xerces-C++

[edit] XQilla

Homepage: http://xqilla.sourceforge.net/HomePage

Description: XQilla is an XQuery and XPath 2 library and command line utility written in C++,implemented on top of the Xerces-C++ library.

Available versions: 2.3.2-intel-2015b

Command: module load XQilla

[edit] x264

Homepage: http://www.videolan.org/developers/x264.html

Description: x264 is a free software library and application for encoding video streams into the H.264/MPEG-4AVC compression format, and is released under the terms of the GNU GPL.

Available versions: 20160614-foss-2016b

Command: module load x264

[edit] x265

Homepage: http://x265.org/

Description: x265 is a free software library and application for encoding video streams into the H.265AVC compression format, and is released under the terms of the GNU GPL.

Available versions: 2.4-foss-2016b

Command: module load x265

[edit] Yasm

Homepage: http://www.tortall.net/projects/yasm/

Description: Yasm: Complete rewrite of the NASM assembler with BSD license

Available versions: 1.3.0-intel-2015b, 1.3.0-foss-2016b

Command: module load Yasm

[edit] zlib

Homepage: http://www.zlib.net/

Description: zlib is designed to be a free, general-purpose, legally unencumbered -- that is,not covered by any patents -- lossless data-compression library for use on virtually anycomputer hardware and operating system.

Available versions: 1.2.10, 1.2.11-GCCcore-6.3.0, 1.2.11-intel-2016a, 1.2.5-goolf-1.4.10, 1.2.5-goolf-1.7.20, 1.2.7-foss-2016a, 1.2.7-goolf-1.4.10, 1.2.7-goolf-1.7.20, 1.2.7-intel-2015b, 1.2.7-intel-2016a, 1.2.8, 1.2.8-GCC-4.9.3-binutils-2.25, 1.2.8-GCCcore-4.9.3, 1.2.8-GCCcore-5.4.0, 1.2.8-GNU-4.9.3-2.25, 1.2.8-foss-2015b, 1.2.8-foss-2016a, 1.2.8-foss-2016b, 1.2.8-goolf-1.4.10, 1.2.8-goolf-1.7.20, 1.2.8-intel-2015b, 1.2.8-intel-2016a, 1.2.8-GCCcore-6.1.0, 1.2.8-intel-2017a, 1.2.11, 1.2.11-GCCcore-6.4.0, 1.2.8-intel-2016b, 1.2.11-GCCcore-7.3.0, 1.2.11-GCCcore-5.4.0, 1.2.9-intel-2017a

Command: module load zlib

[edit] ZeroMQ

Available versions: 3.2.5-intel-2015b, 4.1.4-foss-2016a

Command: module load ZeroMQ